X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 273.0
Details 1.4 M ammonium sulfate, 20 uM BME, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.75 α = 90
b = 95.75 β = 90
c = 82.41 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 273
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-03-20
Diffraction Radiation
Monochromator Protocol
KHOZU double flat crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.11588 ALS 8.3.1

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
2.3 40 96.1 0.061 0.102 -- 3.2 19711 18949 -- -- --

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 2.302 29.225 -- 1.34 -- 18948 973 96.14 -- 0.1903 0.1882 0.2289 --
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 2.3022 2.4235 -- 148 2601 0.2288 0.3032 -- 100.0
X Ray Diffraction 2.4235 2.5753 -- 141 2650 0.1804 0.2045 -- 100.0
X Ray Diffraction 2.5753 2.7739 -- 134 2627 0.1741 0.2542 -- 100.0
X Ray Diffraction 2.7739 3.0528 -- 141 2651 0.1818 0.2356 -- 100.0
X Ray Diffraction 3.0528 3.494 -- 145 2635 0.183 0.2341 -- 99.0
X Ray Diffraction 3.494 4.3996 -- 142 2445 0.1784 0.212 -- 91.0
X Ray Diffraction 4.3996 29.2278 -- 122 2366 0.202 0.2258 -- 84.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.145
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.145
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.29
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.079
f_dihedral_angle_d 18.52
f_angle_d 1.246
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2042
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 92

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction