X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 300.0
Details PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 132.44 α = 90
b = 197.81 β = 90
c = 51.63 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 Double crystal monochromator Si-111 2001-03-28
CCD SBC-2 Double crystal monochromator Si-111 2001-03-07
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator Si-111 SINGLE WAVELENGTH
Double crystal monochromator Si-111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97941 APS 19-ID
SYNCHROTRON APS BEAMLINE 19-ID 0.97925, 0.97938, 0.99187 APS 19-ID

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
1.5 50 95.1 0.087 -- -- 4.0 217343 207448 -- -3.0 16.0
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)
1.5 1.55 81.4 0.24 -- 4.0 2.0 --

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 1.5 48.1 0.0 0.0 207247 207247 10174 95.2 0.199 0.199 0.199 0.213 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 1.5 1.59 -- 1512 28847 0.223 0.245 0.006 84.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 19.0
Anisotropic B[1][1] -1.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.56
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.6
c_improper_angle_d 1.07
c_bond_d 0.006
c_angle_deg 1.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.18
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9367
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 867

Software

Software
Software Name Purpose
d*TREK data scaling
HKL-2000 data reduction
SnB phasing
SOLVE phasing
DM model building
CNS refinement version: 0.9
d*TREK data reduction
HKL-2000 data scaling
DM phasing