6VIM
P. putida mandelate racemase co-crystallized with phenylboronic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UXK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294 | The reservoir solution consisted of PEG 4000 (10% w/v) and Bis-Tris Propane (BTP; 50 mM, pH 7.0). The protein solution consisted of 6 mg/mL P. putida MR, 1.0 mM phenylboronic acid, 3.3 mM MgCl2, and 50 mM HEPES buffer (pH 7.5). The protein solution and reservoir solution were mixed in a 1:1 ratio to a final volume of 10 uL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 59.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 228.988 | α = 90 |
b = 150.356 | β = 129.252 |
c = 150.275 | 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 | RAYONIX MX-300 | 2019-04-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 116.57 | 99.7 | 0.116 | 0.995 | 9.2 | 3.8 | 262707 | 19.69 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.07 | 99.5 | 0.597 | 0.782 | 2.3 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3UXK | 2 | 116.37 | 1.34 | 262591 | 13014 | 99.65 | 0.1602 | 0.1581 | 0.1983 | 22.94 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 3.7933 |
f_angle_d | 0.7574 |
f_chiral_restr | 0.0473 |
f_bond_d | 0.0065 |
f_plane_restr | 0.0052 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21539 |
Nucleic Acid Atoms | |
Solvent Atoms | 3348 |
Heterogen Atoms | 140 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
autoPROC | data reduction |
autoPROC | data scaling |
PHASER | phasing |