X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 0.5M Sodium Chloride, 0.1M Tris-HCl pH8.5, 5% PEG 8000 and 20% 2-methyl-2, 4- pentanediol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 252.3 α = 90
b = 252.3 β = 90
c = 561.2 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 MARMOSAIC 300 mm CCD -- 2015-03-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID

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
4.3 50 82.7 0.132 -- 9.812 4.6 -- 39396 -- -- 127.24
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)
4.3 4.45 50.7 0.903 -- -- 4.2 2382

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 4.301 48.343 -- 2.0 -- 25786 1315 54.9 -- 0.2825 0.2811 0.309 --
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 4.301 4.4731 -- 13 164 0.3523 0.3529 -- 3.0
X Ray Diffraction 4.4731 4.6765 -- 33 470 0.3218 0.3542 -- 10.0
X Ray Diffraction 4.6765 4.9229 -- 45 865 0.322 0.3672 -- 18.0
X Ray Diffraction 4.9229 5.2309 -- 61 1463 0.3025 0.3006 -- 30.0
X Ray Diffraction 5.2309 5.6343 -- 132 2485 0.3185 0.3319 -- 50.0
X Ray Diffraction 5.6343 6.2002 -- 232 4580 0.3433 0.3602 -- 92.0
X Ray Diffraction 6.2002 7.095 -- 271 4845 0.3337 0.3613 -- 98.0
X Ray Diffraction 7.095 8.9297 -- 273 4819 0.2824 0.3124 -- 97.0
X Ray Diffraction 8.9297 48.3461 -- 255 4780 0.2272 0.2601 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 215.777
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.8
f_plane_restr 0.005
f_chiral_restr 0.067
f_bond_d 0.006
f_angle_d 1.196
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22452
Nucleic Acid Atoms 0
Heterogen Atoms 1486
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement
HKL-2000 data collection
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction
PHASER phasing