X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details sodium cacodylate, PEG 8000, glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.67 α = 90
b = 80.68 β = 105.33
c = 107.85 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 133
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-06-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 -- SPring-8 BL12B2

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
3.18 28.54 98.3 0.124 -- -- 15.0 20087 19692 -- -3.0 --
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)
3.2 3.24 99.9 0.472 -- -- -- --

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 3.2 28.54 -- 0.0 19764 18485 1817 93.5 -- -- 0.264 0.348 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 3.2 3.35 2264 236 2028 0.378 0.482 0.023 92.3
X Ray Diffraction 3.35 3.52 2313 206 2107 0.308 0.447 0.021 93.9
X Ray Diffraction 3.52 3.74 2141 206 1935 0.323 0.432 0.022 87.1
X Ray Diffraction 3.74 4.03 2299 222 2077 0.225 0.331 0.015 93.8
X Ray Diffraction 4.03 4.43 2037 210 1827 0.229 0.295 0.016 83.3
X Ray Diffraction 4.43 5.07 2454 249 2205 0.2 0.269 0.013 99.0
X Ray Diffraction 5.07 6.38 2459 241 2218 0.298 0.397 0.018 98.9
X Ray Diffraction 6.38 28.54 2518 247 2271 0.273 0.338 0.018 99.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 82.68
Anisotropic B[1][1] 20.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 22.99
Anisotropic B[2][2] -9.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.11
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.5
c_bond_d 0.01
c_dihedral_angle_d 24.3
c_improper_angle_d 0.96
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.43
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.64
Luzzati Sigma A (R-Free Set) 0.88
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7674
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 12

Software

Software
Software Name Purpose
ADSC data collection
SCALEPACK data scaling
CNS refinement
CNS phasing