X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details PROTEIN WAS CRYSTALLIZED FROM 12% PEG 20000, 100 MM MES, PH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.9 α = 90
b = 89.6 β = 90
c = 116 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1997-02-13
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.65 15 96.5 -- 0.095 -- 3.7 -- 21379 -- -- 47.2
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)
2.65 2.71 96.4 -- 0.44 2.6 2.5 --

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 2.65 15.0 -- 0.0 -- 21207 1666 96.7 -- 0.206 0.206 0.276 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 2.65 2.82 -- 293 3143 0.304 0.358 0.021 95.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.1
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.83
x_scbond_it 2.57
x_mcangle_it 2.92
x_mcbond_it 1.75
x_improper_angle_d 1.04
x_bond_d 0.006
x_angle_deg 1.3
x_dihedral_angle_d 26.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4957
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 108

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK 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
SCALEPACK data reduction
DENZO data collection