X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details PROTEIN WAS CRYSTALLIZED FROM 12% PEG 20K, 100 MM MES BUFFER, PH 6.5, 10 MM DTT

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.82 α = 90
b = 64.38 β = 90
c = 87.16 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PRINCETON 2K CRYSTALS 1997-06
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F2 -- CHESS F2

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
1.79 24.9 80.4 -- 0.046 -- 3.5 -- 29818 -- 2.0 20.3
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)
1.79 1.83 42.9 -- 0.324 2.7 2.0 --

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
MULTIWAVELENGTH ANOMALOUS DIFFRACTION 1.8 5.0 -- 2.0 -- 24149 1668 78.4 -- 0.188 0.188 0.23 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 1.8 1.91 -- 129 1829 0.255 0.269 0.024 38.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.8
Anisotropic B[1][1] 0.85
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.86
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 18.62
x_scbond_it 22.9
x_mcangle_it 2.9
x_mcbond_it 1.94
x_improper_angle_d 1.24
x_bond_d 0.008
x_angle_deg 1.3
x_dihedral_angle_d 20.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2317
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 102

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASES, X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building
PHASES model building
SCALEPACK data reduction
DENZO data collection