X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 289.0
Details 1.8M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate (pH 5.0)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 347.9 α = 90
b = 347.9 β = 90
c = 347.9 γ = 90
Symmetry
Space Group P 42 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN A200 -- 2014-07-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1

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
2.5 50 100.0 0.217 -- -- 12.7 -- 244135 -- -- 15.0
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)
2.5 2.59 100.0 0.796 -- 4.1 10.2 --

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
-- 2.5 49.7 -- 0.0 -- 244027 12014 99.9 -- 0.164 0.164 0.172 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 2.5 2.59 -- 1240 22644 0.268 0.28 0.008 98.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 24.1
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 9.16
c_scangle_it 10.48
c_mcangle_it 6.73
c_angle_deg 1.6
c_improper_angle_d 1.06
c_bond_d 0.01
c_dihedral_angle_d 26.2
c_mcbond_it 5.29
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6113
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 506

Software

Software
Software Name Purpose
CNS refinement version: 1.3
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing