1HE2
Human biliverdin IX beta reductase: NADP/biliverdin IX alpha ternary complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HDO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 30% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5. NADP ADDED TO A FINAL CONCENTRATION OF 2.5 MM |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 40.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.2 | α = 90 |
b = 49.2 | β = 90 |
c = 106.9 | 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 | 1999-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
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 | 1.2 | 29.9 | 97.5 | 0.042 | 10.2 | 4.3 | 65438 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.2 | 1.26 | 97.6 | 0.188 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1HDO | 1.2 | 20 | 65424 | 3304 | 97.3 | 0.128 | 0.122 | 0.159 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
15 | 1493.16 | 1870.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.062 |
s_non_zero_chiral_vol | 0.035 |
s_angle_d | 0.033 |
s_zero_chiral_vol | 0.027 |
s_from_restr_planes | 0.0264 |
s_similar_adp_cmpnt | 0.025 |
s_anti_bump_dis_restr | 0.022 |
s_bond_d | 0.014 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1544 |
Nucleic Acid Atoms | |
Solvent Atoms | 287 |
Heterogen Atoms | 91 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |