X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.4
Temperature 293.0
Details PEG4000, PEG6000, sodium acetate, sodium chloride, TRIS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 220.16 α = 90
b = 220.16 β = 90
c = 113.12 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2001-01-01
CCD MARRESEARCH mirrors --
Diffraction Radiation
Monochromator Protocol
Si(111) MAD
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9795, 0.9798, 0.9733, 0.9839 SPRING-8 BL41XU
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPRING-8 BL41XU

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
3.5 50 99.0 0.075 0.075 -- -- 293584 293584 -- -- 71.3
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)
3.5 3.71 98.6 0.27 0.27 5.1 -- --

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
MAD 3.3 10.0 -- 0.0 -- 44854 2239 98.0 -- 0.258 0.255 0.326 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 3.3 3.5 6103 360 6616 0.31 0.37 0.02 91.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 82.5
Anisotropic B[1][1] -9.51
Anisotropic B[1][2] 15.74
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -9.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 19.03
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.78
c_bond_d 0.006
c_angle_deg 1.4
c_dihedral_angle_d 25.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.5
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.54
Luzzati Sigma A (R-Free Set) 0.75
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8673
Nucleic Acid Atoms 0
Heterogen Atoms 140
Solvent Atoms 79

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
MLPHARE model building
SCALEPACK data reduction
DENZO data collection