2XIL
The structure of cytochrome c peroxidase Compound I
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2V2E | PDB ENTRY 2V2E |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | KPI 50 MM PH 6.5, MPD 30% (V/V) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 52 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 51.04 | ¦Á = 90 |
b = 75.04 | ¦Â = 90 |
c = 106.8 | ¦Ã = 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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 1.67 | 1.76 | 92 | 0.07 | 10.9 | 2.9 | 40890 |
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 | 1.67 | 1.76 | 81 | 0.24 | 3.8 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2V2E | 1.68 | 33.11 | 40890 | 2186 | 91.25 | 0.15535 | 0.15298 | 0.19937 | RANDOM | 22.798 |
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] | |
0.02 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.659 |
r_dihedral_angle_4_deg | 26.136 |
r_dihedral_angle_3_deg | 15.627 |
r_scangle_it | 7.653 |
r_scbond_it | 5.621 |
r_dihedral_angle_1_deg | 5.577 |
r_mcangle_it | 4.577 |
r_mcbond_it | 3.273 |
r_angle_refined_deg | 2.182 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2369 |
Nucleic Acid Atoms | |
Solvent Atoms | 684 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CCP4 | phasing |