1Z3P
X-Ray crystal structure of a mutant Ribonuclease S (M13Nva)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2RLN | PDB Entry 2RLN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Batch method | 5.2 | 293 | ammonium sulfate, cesium chloride, sodium acetate, pH 5.2, Batch method, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.38 | α = 90 |
b = 44.38 | β = 90 |
c = 97.459 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 293 | IMAGE PLATE | MARRESEARCH | 2003-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 2 | 20 | 97.1 | 0.067 | 7.4 | 8125 | 7872 | 24.4 |
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) | |||||||||||
2 | 2.07 | 91.5 | 0.195 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry 2RLN | 2 | 14.96 | 8125 | 7818 | 357 | 98.3 | 0.189 | 0.189 | 0.18 | 0.233 | 0.23 | RANDOM | 27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.7 |
c_scangle_it | 3.6 |
c_mcangle_it | 2.51 |
c_scbond_it | 2.36 |
c_mcbond_it | 1.56 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.68 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 924 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |