3KW3
Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2DY3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 289 | Native crystal grown in 0.1 M Hepes pH 8.0, 33% PEG 3350 at 42.3 mg/mL, crystal tracking ID 203636d11; crystal used for combined Phaser MR/IodoSAD grown in 0.1 M Hepes pH 8.5, 0.2 M MgCl2, 25% PEG 3350 and soaked for 1 hour in 0.1 M Hepes pH 8.0, 1.0 M KI, 35% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.794 | α = 90 |
b = 54.316 | β = 112.39 |
c = 107.476 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2009-07-11 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2009-11-16 | M | SINGLE WAVELENGTH | ||||||
1,2 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 0.976484 | ALS | 5.0.3 |
2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1,2 | 2.04 | 50 | 99.5 | 0.088 | 17.4 | 5.3 | 45971 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2 | 2.04 | 2.12 | 96.7 | 0.496 | 2.79 | 4.6 | 4405 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD, MR | THROUGHOUT | 2DY3 | 2.04 | 34.9 | 45875 | 2318 | 98.54 | 0.193 | 0.191 | 0.233 | RANDOM | 22.817 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.82 | -1.88 | -1.01 | 0.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.335 |
r_dihedral_angle_4_deg | 16.392 |
r_dihedral_angle_3_deg | 15.135 |
r_dihedral_angle_1_deg | 6.391 |
r_scangle_it | 3.061 |
r_scbond_it | 1.954 |
r_angle_refined_deg | 1.408 |
r_mcangle_it | 1.167 |
r_mcbond_it | 0.664 |
r_chiral_restr | 0.088 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5407 |
Nucleic Acid Atoms | |
Solvent Atoms | 426 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELXD | phasing |