4JHM
Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme from Pseudovibrio sp.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3SJN | PDB ENTRY 3SJN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 30% PEG 8000, 100mM Imidazole/Hydrochloric acid pH 8.0, 200mM sodium chloride, Vapor diffusion, Sitting drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 201.793 | α = 90 |
b = 117.313 | β = 99.77 |
c = 143.127 | 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 315r | 2011-06-16 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.978 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.8 | 55.536 | 96 | 0.053 | 0.095 | 8.8 | 3.7 | 77549 | 77549 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.8 | 2.95 | 92.5 | 0.379 | 0.379 | 2 | 3.4 | 10798 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3SJN | 2.8 | 39.41 | 75912 | 75912 | 3989 | 98.57 | 0.1971 | 0.1941 | 0.253 | RANDOM | 85.245 |
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] | |
-0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.813 |
r_dihedral_angle_4_deg | 16.698 |
r_dihedral_angle_3_deg | 14.909 |
r_dihedral_angle_1_deg | 5.162 |
r_mcangle_it | 4.554 |
r_mcbond_it | 3.012 |
r_mcbond_other | 3.012 |
r_angle_refined_deg | 0.83 |
r_angle_other_deg | 0.581 |
r_chiral_restr | 0.052 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23530 |
Nucleic Acid Atoms | |
Solvent Atoms | 8 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
MOSFLM | data reduction |
MOLREP | phasing |