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_scangle_it 4.32
x_scbond_it 3.15
x_mcangle_it 2.79
x_mcbond_it 2.03
x_torsion_impr_deg 0.86
x_torsion_deg 18.5
x_angle_deg 1.2
x_bond_d 0.007
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 8512
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 669

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement