1HJT
SPERM WHALE MYOGLOBIN (FERROUS, NITRIC OXIDE BOUND)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YOI | PDB ENTRY 1YOI |
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 34.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.453 | α = 90 |
b = 29.444 | β = 106.32 |
c = 35.328 | 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 | 295 | IMAGE PLATE | RIGAKU | 1997-03-10 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | SIEMENS |
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 | 1.7 | 30 | 80.1 | 0.044 | 32.7 | 3.1 | 11674 |
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) | |||||||||||
1.7 | 1.8 | 73.1 | 0.244 | 6.4 | 2.5 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | FREE R | PDB ENTRY 1YOI | 1.7 | 5 | 10947 | 1094 | 79.9 | 0.1663 | 0.1617 | 0.2515 |
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 |
1352.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.105 |
s_zero_chiral_vol | 0.042 |
s_non_zero_chiral_vol | 0.041 |
s_angle_d | 0.017 |
s_from_restr_planes | 0.015 |
s_anti_bump_dis_restr | 0.006 |
s_bond_d | 0.005 |
s_similar_dist | 0.004 |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1217 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
SHELXL-96 | model building |
X-PLOR | model building |
SHELXL-96 | refinement |
X-PLOR | refinement |
XDS | data reduction |
XSCALE | data scaling |
SHELXL-96 | phasing |
X-PLOR | phasing |