4XA8
Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KBO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 0.2 UL OF 11 MG/ML PROTEIN IN 20 MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 0.1% SODIUM AZIDE, 0.5 MM TCEP and 10 mM NADH WERE MIXED WITH 0.2 UL OF THE TOP96 CONDITION #34 (0.2M MAGNESIUM CHLORIDE, 6-HYDRATE, 0.1M HEPES, 25%W/V PEG 3350 PH=7.5) AND EQUILIBRATED AGAINST 1.5 M NACL SOLUTION IN 96 WELL 3 DROP CRYSTALLIZATION PLATE (SWISSCI). BEFORE CRYSTALLIZATION PROTEIN WAS INCUBATED WITH 1/50 V/V OF 1 MG/ML TEV SOLUTION AT 289 K FOR 1 HOUR |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 41.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.762 | α = 90 |
b = 63.714 | β = 90 |
c = 154.967 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | MARMOSAIC 300 mm CCD | Beryllium Lenses | 2014-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.978 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.9 | 50 | 95.2 | 0.069 | 0.073 | 0.023 | 21.738 | 9 | 22335 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 1.93 | 96.9 | 0.835 | 0.881 | 0.276 | 0.786 | 2.6 | 9.6 | 1110 |
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 | 3KBO | 1.9 | 50 | 22262 | 1098 | 95.2 | 0.1655 | 0.1632 | 0.2086 | RANDOM | 39.663 |
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 | -1.24 | 2.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.127 |
r_dihedral_angle_4_deg | 16.421 |
r_dihedral_angle_3_deg | 13.682 |
r_dihedral_angle_1_deg | 5.555 |
r_mcangle_it | 2.154 |
r_angle_refined_deg | 1.639 |
r_mcbond_it | 1.518 |
r_mcbond_other | 1.518 |
r_angle_other_deg | 0.837 |
r_chiral_restr | 0.093 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2270 |
Nucleic Acid Atoms | |
Solvent Atoms | 173 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
BLU-MAX | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |
HKL-3000 | phasing |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |