X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.75
Details THE RNASE S CRYSTAL HAS BEEN STABILIZED BY GLUTARALDEHYDE CROSSLINKING AND THEN THE CRYSTAL HAS BEEN SOAKED IN 5M UREA., pH 4.75 DATA COLLECTED ON A CRYSTAL SOAKED IN 5M UREA. THE CRYSTAL WAS STABILIZED BY GLUTARALDEHYDE CROSSLINKING

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.8 α = 90
b = 44.8 β = 90
c = 98.62 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE -- MIRRORS --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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
3 15 76.6 0.09 -- -- 2.5 -- 2233 -- -- 53.1
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.0 3.2 49.3 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.0 15.0 -- 1.0 -- 2233 245 76.6 -- -- 0.175 0.253 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.0 3.19 -- 37 161 0.217 0.237 0.039 49.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.2
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 12.84
x_scbond_it 9.22
x_mcangle_it 9.58
x_mcbond_it 6.26
x_improper_angle_d 1.05
x_bond_d 0.011
x_angle_deg 1.2
x_dihedral_angle_d 24.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 4.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 905
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 7

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
MARSCALE Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
AMORE model building
MARSCALE data reduction
XDS data collection