5B4Z
Crystal structure of heme binding protein HmuT H141A mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 2.25 M Ammonium sulfate, 0.20 M Potassium thiocyanate, 0.20 M Ammonium tartrate, 5%(v/v) Polypropylene glycol, 0.025%(w/v) beta-Octyl glucoside |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.38 | α = 90 |
b = 73.38 | β = 90 |
c = 147.42 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | RAYONIX MX300HE | 2014-06-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.90 | SPring-8 | BL44XU |
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 | 1.3 | 48.94 | 98.8 | 0.058 | 19.98 | 9.58 | 97636 |
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 | 1.3 | 1.34 | 96.6 | 0.551 | 3.73 |
Refinement
Statistics | |||||||||||||||||||
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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 | 5az3 | 1.3 | 48.94 | 92836 | 4800 | 98.8 | 0.15195 | 0.15106 | 0.16894 | RANDOM | 14.139 |
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] | |
-0.07 | -0.07 | 0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.711 |
r_sphericity_free | 17.901 |
r_dihedral_angle_4_deg | 12.789 |
r_dihedral_angle_3_deg | 10.391 |
r_dihedral_angle_1_deg | 5.819 |
r_sphericity_bonded | 5.202 |
r_long_range_B_refined | 1.894 |
r_long_range_B_other | 1.662 |
r_angle_refined_deg | 1.318 |
r_scangle_other | 1.228 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2239 |
Nucleic Acid Atoms | |
Solvent Atoms | 230 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |