4NKP
Crystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 277 | 2.4M ammonium sulfate, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.964 | α = 90 |
b = 80.964 | β = 90 |
c = 72.927 | γ = 90 |
Symmetry | |
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Space Group | P 4 |
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 | PIXEL | DECTRIS PILATUS 6M | Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | 2013-05-01 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837,0.97879,0.97812 | SSRL | BL11-1 |
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 | 1.24 | 28.625 | 96.3 | 0.033 | 14.7 | 131689 | -3 | 11.502 |
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 | 1.24 | 1.28 | 92.2 | 0.539 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.24 | 28.625 | 131689 | 6635 | 99.24 | 0.1291 | 0.128 | 0.1494 | RANDOM | 17.4296 |
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] | |
-0.14 | -0.14 | 0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.263 |
r_dihedral_angle_4_deg | 18.737 |
r_dihedral_angle_3_deg | 12.819 |
r_dihedral_angle_1_deg | 5.325 |
r_scangle_it | 4.693 |
r_sphericity_free | 3.999 |
r_scbond_it | 3.093 |
r_sphericity_bonded | 2.384 |
r_mcangle_it | 2.342 |
r_mcbond_it | 1.52 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4140 |
Nucleic Acid Atoms | |
Solvent Atoms | 559 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SOLVE | phasing |
XSCALE | data scaling |
REFMAC | refinement |
XDS | data reduction |