X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details ammonium sulfate, sodium citrate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.99 α = 90
b = 64.99 β = 90
c = 156.4 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V -- 2001-11-14
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL24XU 0.836 SPRING-8 BL24XU

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 35 95.9 0.069 0.06 -- 4.1 22362 22310 -- 3.0 38.25
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)
2.0 2.11 97.4 0.529 0.459 1.6 4.0 3243

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
MOLECULAR REPLACEMENT 2.0 35.0 -- 0.0 22295 22295 2211 94.9 -- -- 0.2698 0.2986 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 2.0 2.07 2220 206 -- 0.2665 0.2934 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 29.84
Anisotropic B[1][1] -1.362
Anisotropic B[1][2] -1.362
Anisotropic B[1][3] 2.725
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_improper_angle_d 0.70793
c_dihedral_angle_d 25.4929
c_angle_deg 1.24735
c_bond_d 0.006089
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.07
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1894
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 42

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
CNS model building
SCALA data reduction
R-AXIS data collection