X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details HEPES-Na, tri-Sodium Citrate dihydrate, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 152.6 α = 90
b = 152.6 β = 90
c = 119.36 γ = 120
Symmetry
Space Group P 6 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-01-01
CCD MARRESEARCH -- 2001-01-01
Diffraction Radiation
Monochromator Protocol
rotated-inclined fixed exit double crystal SINGLE WAVELENGTH
rotated-inclined fixed exit double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.979713 SPring-8 BL41XU
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9798,0.9800,0.9742,0.9839 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 41.33 98.5 -- -- -- -- 16587 16587 -- 0.0 --
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)
3.0 3.05 85.4 -- -- -- -- --

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 3.0 40.0 -- 0.0 16587 16586 816 -- -- -- 0.238 0.286 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 3.0 3.05 -- -- -- 0.523 -- -- --
X Ray Diffraction 3.05 3.11 -- -- -- 0.496 -- -- --
X Ray Diffraction 3.11 3.17 -- -- -- 0.476 -- -- --
X Ray Diffraction 3.17 3.23 -- -- -- 0.376 -- -- --
X Ray Diffraction 3.23 3.3 -- -- -- 0.302 -- -- --
X Ray Diffraction 3.3 3.38 -- -- -- 0.284 -- -- --
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.0316
c_improper_angle_d 2.6685
c_angle_d 3.16095
c_dihedral_angle_d 22.8239
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.69
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.54
Luzzati Sigma A (R-Free Set) 0.82
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1816
Nucleic Acid Atoms 808
Heterogen Atoms 0
Solvent Atoms 131

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MLPHARE phasing
CNS refinement version: 1.0