X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details 50mM magnesium acetate, 200mM ammonium sulphate, 20% PEG4000, 100mM acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.84 α = 90
b = 89.75 β = 90
c = 170.74 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 ADSC QUANTUM 4 -- 2000-09-28
CCD ADSC QUANTUM 4 -- 2000-06-08
Diffraction Radiation
Monochromator Protocol
CARS-design Si(111) double-bounce MAD
Double Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.9117 NSLS X4A
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9788, 0.9790, 0.9537 APS 14-BM-D

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
2.25 45.94 98.8 0.066 -- -- 4.7 57710 57710 0.0 0.0 24.8
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)
2.25 2.33 100.0 0.198 -- 8.0 -- --

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 2.25 45.94 0.0 0.0 56830 56830 2877 98.6 0.231 0.231 0.227 0.26 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 2.25 2.39 -- 487 8945 0.243 0.295 0.013 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 48.1
Anisotropic B[1][1] -2.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.0
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 5.74
c_angle_deg 1.1
c_improper_angle_d 1.05
c_scbond_it 4.67
c_bond_d 0.007
c_mcbond_it 3.0
c_dihedral_angle_d 19.7
c_mcangle_it 4.09
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4215
Nucleic Acid Atoms 2202
Heterogen Atoms 0
Solvent Atoms 484

Software

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