1RTU
USTILAGO SPHAEROGENA RIBONUCLEASE U2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RNT | RNASE T1 (PDB ENTRY 1RNT) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | CRYSTALS WERE PREPARED BY HANGING-DROP VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'-CYTIDINE, 0.4M AMMONIUM SULFATE, EQUILIBRATED AGAINST A RESERVOIR OF 0.9M AMMONIUM SULFATE CONTAINING 0.1M ACETATE BUFFER (PH 4.5)., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.32 | α = 90 |
b = 61.27 | β = 90 |
c = 34.95 | γ = 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 | 284 | IMAGE PLATE | FUJI | DOUBLE FOCUSSING MIRROR | 1990-05-22 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY | Photon Factory |
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 | 1.8 | 12 | 96.1 | 0.0342 | 4 | 9903 | 1 |
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 | 1.8 | 1.87 | 86.4 | 0.077 | 3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | RNASE T1 (PDB ENTRY 1RNT) | 1.8 | 8 | 9807 | 9807 | 96.5 | 0.143 | 13.4 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 25.2 |
p_staggered_tor | 12.4 |
p_scangle_it | 2.72 |
p_planar_tor | 2.6 |
p_scbond_it | 1.73 |
p_mcangle_it | 1.214 |
p_mcbond_it | 0.76 |
p_xyhbond_nbd | 0.173 |
p_chiral_restr | 0.17 |
p_singtor_nbd | 0.157 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 870 |
Nucleic Acid Atoms | |
Solvent Atoms | 141 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
OSCMGR | data collection |
TOMOKO | data reduction |
MARIKO | data reduction |
X-PLOR | model building |
PROLSQ | refinement |
X-PLOR | refinement |
OSC | data reduction |
A | data scaling |
MARIKO | data scaling |
X-PLOR | phasing |