1FDV
HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH NAD+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FDT | PDB ENTRY 1FDT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.3 | PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NAD+, 100 MM NACL; THEN SOAKED IN 27 % GLYCEROL, 2.3 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.1, 80 MM NACL, 1 MM NAD+ |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.96 | 69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.12 | α = 90 |
b = 79.11 | β = 91.93 |
c = 120.47 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 130 | CCD | ESRF | MIRRORS | 1995-11-16 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM02 | ESRF | BM02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 3 | 40 | 91.6 | 0.146 | 3.61 | 56921 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
3.1 | 3.2 | 98.5 | 0.418 | 3.94 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1FDT | 3.1 | 10 | 2 | 30594 | 1594 | 83 | 0.219 | 0.295 | RANDOM | 25.33 |
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 |
p_chiral_restr | 0.246 |
p_planar_d | 0.059 |
p_angle_d | 0.043 |
p_bond_d | 0.017 |
p_plane_restr | 0.016 |
p_angle_deg | |
p_hb_or_metal_coord | |
p_mcbond_it | |
p_mcangle_it | |
p_scbond_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8568 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 176 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
REFMAC | refinement |
XDS | data reduction |