3NML
Sperm whale myoglobin mutant H64W carbonmonoxy-form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2MBW | PDB ENTRY 2MBW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Batch Method | 9 | 293 | Protein solution (20mg/ml protein in 0.02m Tris-HCl ph9.0) mixed with mother liquor (3.2m ammonium sulphate, 0.05m tris-hcl, ph9.0) for final concentrations of 2.5m ammonium sulphate, Batch Method, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.93 | α = 90 |
b = 46.96 | β = 90 |
c = 89.5 | 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 | IMAGE PLATE | RIGAKU RAXIS | 2009-04-10 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 1.68 | 41.59 | 98.9 | 0.041 | 19.7 | 3.71 | 19145 | 3 |
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) | |||||||||||
1.68 | 1.74 | 94.7 | 0.159 | 7 | 3.2 | 1788 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 2MBW | 1.68 | 22.711 | 1 | 19099 | 1909 | 98.72 | 0.1689 | 0.1658 | 0.196 | RANDOM | 20.653 |
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] | |
1.2507 | -0.9086 | -0.342 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.89 |
f_angle_d | 1.242 |
f_chiral_restr | 0.064 |
f_bond_d | 0.019 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1229 |
Nucleic Acid Atoms | |
Solvent Atoms | 233 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
CNS | refinement |
d*TREK | data scaling |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
d*TREK | data reduction |
CNS | phasing |