X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details sodium acetate, PEG 4000, Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.09 α = 90
b = 53.36 β = 90
c = 149.81 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 mirror 2002-02-12
CCD SBC-2 mirror 2002-09-01
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97905, 0.97924, 0.9372 APS 19-ID
SYNCHROTRON APS BEAMLINE 19-ID 0.97932 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
1.75 40.47 98.6 0.047 -- -- 6.5 40030 40030 0.0 0.0 18.3
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)
1.75 1.81 97.9 0.369 -- 3.0 6.5 3918

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
autoSHARP 1.75 40.47 -- 0.0 36801 36801 3710 92.5 0.212 0.209 0.209 0.236 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 1.75 1.83 7889 851 4884 0.254 0.252 0.009 83.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.2
Anisotropic B[1][1] -5.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.16
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 3.1
c_angle_deg 1.2
c_bond_d 0.005
c_scangle_it 4.57
c_scbond_it 2.99
c_improper_angle_d 0.75
c_mcbond_it 1.97
c_dihedral_angle_d 22.2
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2837
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 253

Software

Software
Software Name Purpose
d*treck/HKL2000 data collection
HKL-2000 data reduction
autoSHARP phasing
CNS refinement version: 1.0
d*TREK data reduction
HKL-2000 data scaling