5C7H
Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4XAP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate Tribasic pH 7.0, 20% (w/v) PEG 3350) 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 |
2.24 | 45.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.049 | α = 90 |
b = 78.669 | β = 90 |
c = 79.537 | 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 | MARMOSAIC 300 mm CCD | Beryllium Lenses | 2015-04-16 | 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) | R Sym 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 | 1.3 | 50 | 99.9 | 0.052 | 0.02 | 0.057 | 0.023 | 9.2 | 5.9 | 68811 | 68759 | -3 | 12.1 |
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 | 1.3 | 1.32 | 100 | 0.67 | 0.744 | 0.318 | 0.749 | 2.1 | 5.4 | 3380 |
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 | 4XAP | 1.3 | 50 | 65197 | 3483 | 99.9 | 0.1165 | 0.1152 | 0.1401 | RANDOM | 15.157 |
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] | |
0.06 | -0.16 | 0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.524 |
r_sphericity_free | 24.475 |
r_dihedral_angle_4_deg | 16.474 |
r_sphericity_bonded | 11.664 |
r_dihedral_angle_3_deg | 11.076 |
r_dihedral_angle_1_deg | 5.461 |
r_angle_other_deg | 1.966 |
r_mcangle_it | 1.705 |
r_angle_refined_deg | 1.46 |
r_mcbond_it | 1.332 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2107 |
Nucleic Acid Atoms | |
Solvent Atoms | 432 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
HKL-3000 | phasing |
MLPHARE | phasing |
SHELX | phasing |
HKL-3000 | data scaling |
HKL-3000 | data reduction |
BLU-MAX | data collection |