3VD4
E. coli (lacZ) beta-galactosidase (N460D) in complex with IPTG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JYX | PDB ENTRY 1JYX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 288 | 10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 52.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 151.762 | α = 90 |
b = 162.446 | β = 90 |
c = 203.36 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 210 | 2006-09-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11587 | ALS | 8.3.1 |
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 | 204.12 | 93 | 0.069 | 10.5 | 3.5 | 312850 | 312850 | 19.2 |
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 | 2.11 | 67.1 | 0.371 | 2.5 | 1.9 | 32465 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1JYX | 2 | 110.9 | 308138 | 308138 | 4492 | 100 | 0.17269 | 0.17269 | 0.17213 | 0.21199 | CONSISTENT WITH PREVIOUS STRUCTURES | 25.369 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.14 | -0.27 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.617 |
r_dihedral_angle_4_deg | 14.432 |
r_dihedral_angle_3_deg | 12.506 |
r_dihedral_angle_1_deg | 6.065 |
r_scangle_it | 6.033 |
r_scbond_it | 4.295 |
r_mcangle_it | 2.975 |
r_mcbond_it | 2 |
r_angle_refined_deg | 1.048 |
r_chiral_restr | 0.073 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 32628 |
Nucleic Acid Atoms | |
Solvent Atoms | 3300 |
Heterogen Atoms | 355 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |