X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 290.0
Details 1.0 M succinic acid (pH 7.0), 0.1 M HEPES (pH 7.0), 1% PEG monomethylether 2000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 215.31 α = 90
b = 215.31 β = 90
c = 480.68 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 2014-11-02
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.978720 APS 21-ID-D

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
3.6 50 100.0 0.33 -- 6.803 16.4 -- 149778 -- -- 100.57
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)
3.6 3.66 100.0 -- -- -- 6.2 7392

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 3.6 49.217 -- 1.34 -- 149621 2004 99.95 -- 0.2386 0.2381 0.2737 Random selection
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 3.6 3.69 -- 144 10366 0.3652 0.3993 -- 100.0
X Ray Diffraction 3.69 3.7897 -- 140 10419 0.3523 0.4366 -- 100.0
X Ray Diffraction 3.7897 3.9012 -- 138 10475 0.3293 0.3796 -- 100.0
X Ray Diffraction 3.9012 4.0271 -- 144 10416 0.3097 0.3056 -- 100.0
X Ray Diffraction 4.0271 4.1709 -- 140 10463 0.2869 0.3721 -- 100.0
X Ray Diffraction 4.1709 4.3378 -- 143 10490 0.2649 0.2936 -- 100.0
X Ray Diffraction 4.3378 4.5351 -- 140 10453 0.249 0.2734 -- 100.0
X Ray Diffraction 4.5351 4.7741 -- 144 10553 0.2397 0.2947 -- 100.0
X Ray Diffraction 4.7741 5.0729 -- 144 10504 0.2317 0.2608 -- 100.0
X Ray Diffraction 5.0729 5.4641 -- 143 10524 0.2315 0.2412 -- 100.0
X Ray Diffraction 5.4641 6.0131 -- 142 10601 0.2399 0.3525 -- 100.0
X Ray Diffraction 6.0131 6.8812 -- 147 10603 0.2217 0.2599 -- 100.0
X Ray Diffraction 6.8812 8.6619 -- 141 10718 0.1927 0.2127 -- 100.0
X Ray Diffraction 8.6619 49.2211 -- 154 11032 0.1555 0.175 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.727
f_chiral_restr 0.021
f_bond_d 0.002
f_plane_restr 0.002
f_angle_d 0.478
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 52457
Nucleic Acid Atoms 0
Heterogen Atoms 224
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
SCALEPACK data scaling
PHASER phasing version: 2.5.6
PDB_EXTRACT data extraction version: 3.15
Coot model building version: 0.7
HKL-2000 data reduction version: 2.3.7