X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.5 α = 90
b = 41.27 β = 90
c = 64.56 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
-- -- -- 2011-10-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0 PHOTON FACTORY BL-1A

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
2.7 34.8 -- -- -- -- -- -- 2064 -- -- --

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 2.7 34.77 -- 0.0 -- 2064 187 99.2 -- -- 0.258 0.267 --
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 2.7 2.8 -- 17 180 0.8166 0.8869 -- 100.0
X Ray Diffraction 2.8 2.91 -- 13 187 0.8338 0.011 -- 100.0
X Ray Diffraction 2.91 3.04 -- 16 180 0.5406 0.011 -- 100.0
X Ray Diffraction 3.04 3.2 -- 16 198 0.3212 0.011 -- 100.0
X Ray Diffraction 3.2 3.4 -- 12 178 0.2879 0.011 -- 100.0
X Ray Diffraction 3.4 3.66 -- 24 195 0.1891 0.011 -- 100.0
X Ray Diffraction 3.66 4.03 -- 14 189 0.2313 0.011 -- 100.0
X Ray Diffraction 4.03 4.62 -- 23 184 0.2189 0.011 -- 100.0
X Ray Diffraction 4.62 5.82 -- 25 192 0.2334 0.011 -- 100.0
X Ray Diffraction 5.82 100.0 -- 27 194 0.2602 0.011 -- 93.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.5829
Anisotropic B[1][1] -1.457
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 37.106
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -35.65
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 20.381
c_mcangle_it 20.215
c_scbond_it 21.154
c_mcbond_it 0.0
c_angle_deg 1.16
c_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 484
Heterogen Atoms 2
Solvent Atoms 14

Software

Computing
Computing Package Purpose
CrystalClear Data Reduction (intensity integration)
CrystalClear Data Reduction (data scaling)
Phenix Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
CNS refinement