X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG 6000, MPD, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.81 α = 90
b = 109.62 β = 90
c = 138.28 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 bent cylindrical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator 2000-05-27
Diffraction Radiation
Monochromator Protocol
bend cylindrical Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C

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
1.4 85.9 88.9 0.088 -- -- 5.8 158223 148337 0.0 0.0 14.6
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)
1.5 1.55 56.0 0.331 -- 3.3 2.5 9246

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 1.5 85.9 1.0 1.0 167398 145650 6888 87.0 -- -- 0.197 0.216 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 1.5 1.57 10705 364 10341 0.256 0.275 0.013 51.6
X Ray Diffraction 1.57 1.65 14104 536 13568 0.224 0.238 0.01 68.0
X Ray Diffraction 1.65 1.75 17933 810 17123 0.212 0.244 0.007 86.0
X Ray Diffraction 1.75 1.89 19753 979 18774 0.202 0.233 0.006 94.9
X Ray Diffraction 1.89 2.08 20425 1010 19415 0.196 0.216 0.006 97.8
X Ray Diffraction 2.08 2.38 20759 1035 19724 0.194 0.213 0.006 99.1
X Ray Diffraction 2.38 3.0 20971 1068 19903 0.196 0.214 0.006 99.6
X Ray Diffraction 3.0 85.9 21000 1086 19914 0.186 0.204 0.006 97.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.87
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.29
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.801
c_dihedral_angle_d 24.19
c_angle_deg 1.3
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.18
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8181
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 983

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