3QZP
Staphylococcus aureus IsdA NEAT domain in complex with cobalt-protoporphyrin IX
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 3.5 | 293 | 1.5 M ammonium sulfate, 0.1 M citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.465 | α = 90 |
b = 51.707 | β = 92.08 |
c = 55.747 | 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 | 100 | CCD | MARMOSAIC 225 mm CCD | Vertically focusing mirror | 2007-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97934 | CLSI | 08ID-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 | 1.9 | 50 | 96.6 | 0.091 | 8.3 | 3.3 | 22960 | 14.7 |
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 | 1.9 | 1.93 | 78.1 | 0.341 | 2.5 | 921 |
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 | PDB ENTRY 2ITF | 1.9 | 45 | 22863 | 1174 | 96.44 | 0.1805 | 0.1782 | 0.2225 | RANDOM | 17.6374 |
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] | |
0.57 | -0.84 | -0.87 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.62 |
r_dihedral_angle_4_deg | 21.335 |
r_dihedral_angle_3_deg | 14.368 |
r_dihedral_angle_1_deg | 6.876 |
r_angle_refined_deg | 2.934 |
r_scangle_it | 2.858 |
r_scbond_it | 1.764 |
r_mcangle_it | 1.346 |
r_mcbond_it | 0.72 |
r_chiral_restr | 0.43 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2036 |
Nucleic Acid Atoms | |
Solvent Atoms | 290 |
Heterogen Atoms | 109 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MxDC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |