5XDH
His/DOPA ligated cytochrome c from an anammox organism KSU-1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 3.2M ammonium sulfate, 200mM Potassium sodium tartrate, 100mM Sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.794 | α = 96.46 |
b = 47.687 | β = 99.01 |
c = 48.993 | γ = 102.13 |
Symmetry | |
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Space Group | P 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 | RAYONIX MX300HE | 2016-12-11 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RAYONIX MX300HE | 2014-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 1.7 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.32 | 50 | 96.3 | 0.044 | 0.051 | 0.026 | 16 | 4 | 83160 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.32 | 1.34 | 94.1 | 0.304 | 0.351 | 0.176 | 0.942 | 4 |
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 | SAD | THROUGHOUT | 1.32 | 47.84 | 79049 | 4109 | 96.11 | 0.1559 | 0.1549 | 0.1752 | RANDOM | 14.807 |
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] | |
-0.66 | -0.17 | -0.36 | 0.23 | -0.09 | 0.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.368 |
r_dihedral_angle_4_deg | 22.044 |
r_dihedral_angle_3_deg | 13.011 |
r_dihedral_angle_1_deg | 5.324 |
r_angle_refined_deg | 1.822 |
r_angle_other_deg | 1.26 |
r_chiral_restr | 0.128 |
r_bond_refined_d | 0.015 |
r_gen_planes_other | 0.015 |
r_gen_planes_refined | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2610 |
Nucleic Acid Atoms | |
Solvent Atoms | 512 |
Heterogen Atoms | 195 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
AutoSol | phasing |
HKL | data scaling |