X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 298.15
Details sodium acetate, potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.46 α = 90
b = 128.46 β = 90
c = 136.83 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293.15
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC GRAPHITE-MONOCHROMATER 1998-05-23
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.54180 -- --

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
2.8 50 82.3 0.096 -- -- 2.7 25650 23684 -- 1.0 42.782
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)
2.8 5.1 78.5 0.341 -- -- -- --

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 2.8 50.0 -- 0.0 23684 23684 1152 82.3 -- -- 0.209 0.233 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 2.8 2.93 2022 120 2784 0.42 0.42 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 40.9
Anisotropic B[1][1] 5.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.07
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.95
c_angle_deg 1.172
c_mcangle_it 2.11
c_dihedral_angle_d 22.5
c_mcbond_it 1.2
c_bond_d 0.006
c_scangle_it 3.29
c_improper_angle_d 0.75
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.95
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.93
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3096
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 0

Software

Software
Software Name Purpose
R-AXIS data collection
R-AXIS data reduction
CNS refinement
R-AXIS data scaling
CNS phasing