X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 298.0
Details 100 mM HEPES pH 6.8, 1.2-1.35 M Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 132.16 α = 90
b = 156.68 β = 90
c = 268.44 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal Maxflux Optics 2002-08-02
Diffraction Radiation
Monochromator Protocol
Osmic Confocal Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.6 35 98.1 -- 0.047 -- 3.9 83954 83954 0.0 -3.0 37.3
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)
2.6 2.69 98.1 -- 0.508 2.3 -- --

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
SAD 2.6 30.78 -- 0.0 83954 74865 3836 87.4 0.234 -- 0.232 0.277 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 2.6 2.76 -- 568 10077 0.394 0.426 0.018 75.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 69.5
Anisotropic B[1][1] -20.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 27.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.71
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.62
c_scbond_it 1.62
c_mcangle_it 2.24
c_mcbond_it 1.27
c_improper_angle_d 0.78
c_dihedral_angle_d 21.3
c_angle_deg 1.2
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.66
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 0.73
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10481
Nucleic Acid Atoms 0
Heterogen Atoms 123
Solvent Atoms 666

Software

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