X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 294.0
Details 100 mM MES, pH 5.8, 9% PEG 3350, 4% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.2 α = 90
b = 108.2 β = 90
c = 284.53 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-05-24
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.91939 SSRF BL17U

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
2.74 50 99.6 0.098 -- -- 15.3 26604 24485 1.0 1.0 31.7
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)
2.74 2.84 99.6 0.512 -- 5.1 15.6 2597

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 2.747 46.994 -- 1.33 26604 24485 1246 91.99 -- 0.2016 0.1991 0.249 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 2.7472 2.8572 -- 77 1605 0.257 0.3007 -- 58.0
X Ray Diffraction 2.8572 2.9872 -- 112 2185 0.2503 0.2919 -- 80.0
X Ray Diffraction 2.9872 3.1447 -- 142 2556 0.2581 0.3146 -- 93.0
X Ray Diffraction 3.1447 3.3416 -- 154 2705 0.2362 0.2806 -- 98.0
X Ray Diffraction 3.3416 3.5996 -- 162 2747 0.2142 0.244 -- 99.0
X Ray Diffraction 3.5996 3.9616 -- 156 2754 0.189 0.249 -- 99.0
X Ray Diffraction 3.9616 4.5345 -- 139 2810 0.1487 0.1952 -- 99.0
X Ray Diffraction 4.5345 5.7114 -- 156 2840 0.1667 0.2178 -- 100.0
X Ray Diffraction 5.7114 47.0005 -- 148 3037 0.199 0.2575 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.7443
Anisotropic B[1][2] 2.7443
Anisotropic B[1][3] -5.4885
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.212
f_chiral_restr 0.083
f_dihedral_angle_d 14.987
f_plane_restr 0.005
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4541
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 45

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
HKL-2000 data reduction
HKL-2000 data scaling