X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details 20% MPD, 0.1M Na Cacodylate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 351.39 α = 90
b = 351.39 β = 90
c = 351.39 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-02-12
Diffraction Radiation
Monochromator Protocol
Diamond(111) double-bounce monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 1.107 APS 14-ID-B

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 20 68.0 0.098 0.098 -- 1.6 123514 123514 0.0 0.0 76.4
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 3.62 52.6 0.436 0.436 1.38 1.6 9414

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 + NCS averaging 3.5 20.0 0.0 0.0 123514 104679 1065 62.4 0.313 0.313 0.313 0.316 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 3.5 3.65 9937 109 -- 0.521 0.475 -- 53.0
X Ray Diffraction 3.65 4.08 21064 231 -- 0.458 0.425 -- 56.0
X Ray Diffraction 4.08 4.71 23706 235 -- 0.343 0.324 -- 61.0
X Ray Diffraction 4.71 5.77 22276 237 -- 0.297 0.31 -- 66.0
X Ray Diffraction 5.77 8.16 18558 176 -- 0.207 0.215 -- 71.0
X Ray Diffraction 8.16 20.0 9129 77 -- 0.245 0.284 -- 68.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model individual isotropic
Mean Isotropic B 96.7
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.9
c_bond_d 0.011307
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.8
Luzzati Sigma A (Observed) 1.6
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.7
Luzzati Sigma A (R-Free Set) 1.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4108
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
ENVELOPE model building
CNS refinement
REFMAC refinement
ENVELOPE phasing