4A6G
N-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl methionine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SJA | PDB ENTRY 1SJA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | PROTEIN CONCENTRATION OF 8 MG ML-1 THAT HAD BEEN INCUBATED PREVIOUSLY WITH 10 MM N-ACETYL METHIONINE. CRYSTAL DROPS CONTAINED 100 MM TRIS-HCL (PH 8.0) 15% PEG 4K, 800 MM NA FORMATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.74 | 67.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 216.71 | α = 90 |
b = 216.71 | β = 90 |
c = 261.1 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | 120 | CCD | ADSC CCD | 2011-07-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 |
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 | 2.71 | 88.31 | 100 | 0.08 | 18.6 | 10.2 | 60693 | 4.8 |
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 | 2.71 | 2.79 | 100 | 0.5 | 4.8 | 10.4 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1SJA | 2.71 | 88.31 | 60693 | 3226 | 99.97 | 0.15816 | 0.15535 | 0.21012 | RANDOM | 47.754 |
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] | |
-0.2 | -0.1 | -0.2 | 0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.304 |
r_dihedral_angle_4_deg | 23.185 |
r_dihedral_angle_3_deg | 20.631 |
r_dihedral_angle_1_deg | 6.891 |
r_angle_refined_deg | 2.097 |
r_chiral_restr | 0.138 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10897 |
Nucleic Acid Atoms | |
Solvent Atoms | 265 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |