6PM7
The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | Vapor diffusion with 10 ul drops and 0.6 ml reservoirs. Reservoirs were 6% PEG 3350 buffered with 0.1 M MES at pH 6.5. Drops were equal amounts of 35 mg/ml protein in H2O and reservoir solution. Growth time about two weeks. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 140.865 | α = 90 |
b = 140.865 | β = 90 |
c = 101.84 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | 173 | PIXEL | DECTRIS PILATUS 300K | 2018-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.0 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.85 | 122 | 98.7 | 0.142 | 0.14 | 0.145 | 0.033 | 0.998 | 9.8 | 17.4 | 97987 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.85 | 1.88 | 89.4 | 2.59 | 2.59 | 2.91 | 1.01 | 0.501 | 0.3 | 7.9 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.85 | 121.99 | 92909 | 4940 | 98.54 | 0.19363 | 0.19152 | 0.23248 | RANDOM | 52.633 |
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] | |
-0.91 | -0.46 | -0.91 | 2.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.009 |
r_dihedral_angle_4_deg | 19.86 |
r_dihedral_angle_3_deg | 14.571 |
r_long_range_B_refined | 8.173 |
r_long_range_B_other | 8.164 |
r_dihedral_angle_1_deg | 7.296 |
r_scangle_other | 6.651 |
r_scbond_it | 5.184 |
r_scbond_other | 5.178 |
r_mcangle_it | 4.715 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8016 |
Nucleic Acid Atoms | |
Solvent Atoms | 708 |
Heterogen Atoms | 182 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |