X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details polyethylene glycol monomethylether 5000, Tris-HCl, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 168.6 α = 90
b = 85.3 β = 107.9
c = 115.1 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 1) Cylindrical 1m long collimating mirror (Rh-coated Si) before monochromator 2) Toroidal focusing mirror 1.2m long (Rh-coated zerodur) after the monochromator 2000-06-26
Diffraction Radiation
Monochromator Protocol
Double-Crystal Si 111 crystals SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2

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
2 100 96.7 0.04 -- -- 2.8 107020 101570 -- -3.0 24.3
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)
2.0 2.07 94.9 0.339 -- -- -- --

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 2.0 100.0 -- 0.0 101570 96075 5330 91.5 0.208 0.208 0.206 0.245 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 2.0 2.09 10639 434 10205 0.328 0.329 0.016 81.3
X Ray Diffraction 2.09 2.2 11274 539 10735 0.277 0.278 0.012 86.3
X Ray Diffraction 2.2 2.34 11754 633 11121 0.241 0.242 0.01 89.9
X Ray Diffraction 2.34 2.52 12047 578 11469 0.227 0.226 0.009 91.8
X Ray Diffraction 2.52 2.77 12266 667 11599 0.222 0.221 0.009 93.8
X Ray Diffraction 2.77 3.17 12627 716 11911 0.225 0.225 0.008 96.2
X Ray Diffraction 3.17 4.0 12759 898 11861 0.182 0.183 0.006 96.9
X Ray Diffraction 4.0 76.98 12709 865 11844 0.176 0.175 0.006 95.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 47.05
Anisotropic B[1][1] -1.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -11.69
Anisotropic B[2][2] -0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.52
RMS Deviations
Key Refinement Restraint Deviation
x_mcbond_it 2.03
x_mcangle_it 2.79
x_scangle_it 4.32
x_scbond_it 3.15
x_torsion_deg 18.5
x_angle_deg 1.2
x_bond_d 0.007
x_torsion_impr_deg 0.86
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8685
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 669

Software

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