X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details 0.1M Na-citrate pH 5.0, 14% PEG 4000, 12% Iso-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.56 α = 90
b = 73.56 β = 90
c = 330.01 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-10-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 1.039 NSLS X12B

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 91.6 0.069 -- -- 7.0 -- 85011 -- -- 20.9
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 1.78 58.4 0.354 -- 5.0 -- --

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
AB INITIO PHASING 1.75 36.55 -- 0.0 85011 79683 8029 91.6 -- 0.189 0.189 0.211 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 1.86 -- 885 7677 0.231 0.257 0.009 56.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 24.8
Anisotropic B[1][1] 2.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.45
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.48
c_mcbond_it 1.05
c_mcangle_it 1.51
c_bond_d 0.005
c_improper_angle_d 0.9
c_dihedral_angle_d 22.4
c_angle_deg 1.3
c_scbond_it 1.73
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5453
Nucleic Acid Atoms 0
Heterogen Atoms 104
Solvent Atoms 445

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing