4ZQB
Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 0.2 ul of 10.5 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 Suite 2 condition # 23 (0.1M Bis-Tris, 25%w/v PEG 3350, 0.2M Li sulfate pH=6.5 ) 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 2 mg/ml chymotrypsin and 10 mM NADP solution at 289 K for 3 hours. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.489 | α = 90 |
b = 71.489 | β = 90 |
c = 244.364 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 2014-07-23 | 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 | 1.85 | 50 | 99.3 | 0.161 | 0.161 | 0.171 | 0.073 | 4.7 | 6.2 | 60347 | 59896 | -3 | 23.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.85 | 1.88 | 97.1 | 0.428 | 0.649 | 2 | 6.2 | 2955 |
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 | 3PP8 | 1.85 | 50 | 59625 | 2948 | 99.41 | 0.1665 | 0.1649 | 0.1997 | RANDOM | 27.931 |
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] | |
-0.35 | -0.18 | -0.35 | 1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.836 |
r_dihedral_angle_4_deg | 19.48 |
r_dihedral_angle_3_deg | 12.205 |
r_dihedral_angle_1_deg | 5.439 |
r_angle_refined_deg | 1.565 |
r_angle_other_deg | 1.263 |
r_mcangle_it | 0.938 |
r_mcbond_other | 0.585 |
r_mcbond_it | 0.584 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4762 |
Nucleic Acid Atoms | |
Solvent Atoms | 694 |
Heterogen Atoms | 139 |
Software
Software | |
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Software Name | Purpose |
PDB_EXTRACT | data extraction |
Coot | model building |
REFMAC | refinement |
HKL-3000 | phasing |
MOLREP | phasing |
HKL-3000 | data scaling |
HKL-3000 | data reduction |
BLU-MAX | data collection |