X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 298.0
Details 10% PEG3350, 0.4M NH4SO4,10% Glycerol, pH 7.0, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 159.79 α = 90
b = 159.79 β = 90
c = 683.04 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Cryo-Cooled Si(111) double crystal. 2011-06-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS 0.9798 -- --

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
3.37 50 99.6 0.148 -- -- 2.9 -- 42148 2.0 2.0 --
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)
3.37 3.49 99.9 -- -- -- 2.9 9177

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
MR-SAD 3.37 49.12 -- 0.0 42148 47756 2143 87.72 -- 0.2496 0.2477 0.2858 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 3.37 3.4497 -- 123 2195 0.3732 0.4646 -- 73.0
X Ray Diffraction 3.4497 3.536 -- 122 2286 0.3416 0.3523 -- 76.0
X Ray Diffraction 3.536 3.6316 -- 131 2301 0.3004 0.3324 -- 77.0
X Ray Diffraction 3.6316 3.7384 -- 148 2411 0.282 0.328 -- 81.0
X Ray Diffraction 3.7384 3.859 -- 136 2475 0.2604 0.3377 -- 83.0
X Ray Diffraction 3.859 3.9969 -- 147 2507 0.2324 0.305 -- 83.0
X Ray Diffraction 3.9969 4.1568 -- 138 2562 0.2165 0.2734 -- 85.0
X Ray Diffraction 4.1568 4.3459 -- 140 2670 0.2025 0.2314 -- 88.0
X Ray Diffraction 4.3459 4.5749 -- 141 2781 0.1888 0.219 -- 91.0
X Ray Diffraction 4.5749 4.8613 -- 145 2812 0.1677 0.2538 -- 93.0
X Ray Diffraction 4.8613 5.2362 -- 140 2872 0.1907 0.2328 -- 94.0
X Ray Diffraction 5.2362 5.7624 -- 153 2892 0.2294 0.2527 -- 95.0
X Ray Diffraction 5.7624 6.5946 -- 169 2953 0.2493 0.312 -- 97.0
X Ray Diffraction 6.5946 8.3019 -- 152 3068 0.2372 0.2635 -- 99.0
X Ray Diffraction 8.3019 49.1253 -- 158 3220 0.3058 0.29 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RANDOM
Mean Isotropic B 94.687
Anisotropic B[1][1] 8.4118
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.4118
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -16.8235
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.041
f_bond_d 0.003
f_dihedral_angle_d 14.79
f_angle_d 0.619
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12854
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 21

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.10