3ZV5
CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3-DIHYDROXYBIPHENYL
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BDB | PDB ENTRY 1BDB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SODIUM MALONATE, PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.394 | α = 90 |
b = 75.394 | β = 90 |
c = 173.567 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 225 mm CCD | 2011-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.36 | 50 | 95 | 0.1 | 19.32 | 12.1 | 20162 | 2 | 47.592 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.4 | 69.17 | 99.4 | 0.61 | 2.29 | 7.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 1BDB | 2.4 | 69.17 | 18141 | 982 | 94.18 | 0.21059 | 0.20762 | 0.26568 | RANDOM | 43.265 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.68 | 1.68 | -3.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.95 |
r_dihedral_angle_4_deg | 20.136 |
r_dihedral_angle_3_deg | 19.538 |
r_dihedral_angle_1_deg | 6.497 |
r_scangle_it | 2.744 |
r_scbond_it | 1.803 |
r_angle_refined_deg | 1.776 |
r_mcangle_it | 1.014 |
r_mcbond_it | 0.619 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3978 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |