X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4
Temperature 278.0
Details PEG 8000, potassium phosphate, gluconate 6-phosphate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.67 α = 90
b = 80.23 β = 90
c = 130.04 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 RIGAKU RAXIS IV mirrors 2002-05-30
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU ULTRAX 18 1.5418 -- --

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
2.18 40.12 97.2 0.089 -- -- 7.12 22995 22995 0.0 0.0 20.6
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)
2.18 2.26 97.2 0.207 -- 3.1 7.06 --

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
FOURIER SYNTHESIS 2.18 40.11 -- 0.0 23012 22345 1117 97.1 0.22 0.218 0.218 0.263 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 2.18 2.32 -- 174 3535 0.236 0.293 0.022 98.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.5
Anisotropic B[1][1] 1.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.18
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.09
c_scbond_it 2.14
c_mcangle_it 1.93
c_mcbond_it 1.29
c_improper_angle_d 0.78
c_bond_d 0.006
c_angle_deg 1.4
c_dihedral_angle_d 25.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2983
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 273

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
R-AXIS Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement