X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 298.0
Details 0.1 M Sodium Citrate:HCl pH 5.6, 20% (v/v) 2-Propanol, 20% (w/v) PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.11 α = 90
b = 128.11 β = 90
c = 41.42 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 X 6M -- 2017-06-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-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
2.4 50 99.4 0.109 -- -- 3.2 -- 29670 -- -- 60.8
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)
2.4 2.44 -- 0.759 -- 1.18 2.4 --

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 2.4 41.93 -- 1.97 -- 29638 1557 99.28 -- 0.1657 0.1646 0.1848 --
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 2.4 2.47 -- 135 2527 0.2856 0.3084 -- 97.76
X Ray Diffraction 2.47 2.56 -- 170 2541 0.2704 0.2785 -- 99.52
X Ray Diffraction 2.56 2.67 -- 176 2518 0.2605 0.2721 -- 99.41
X Ray Diffraction 2.67 2.79 -- 122 2590 0.2485 0.2707 -- 99.38
X Ray Diffraction 2.79 2.93 -- 140 2572 0.2272 0.2949 -- 99.74
X Ray Diffraction 2.93 3.12 -- 118 2578 0.2136 0.2604 -- 99.74
X Ray Diffraction 3.12 3.36 -- 162 2523 0.1911 0.2076 -- 99.78
X Ray Diffraction 3.36 3.7 -- 110 2579 0.1692 0.1752 -- 99.45
X Ray Diffraction 3.7 4.23 -- 105 2603 0.1444 0.1513 -- 99.49
X Ray Diffraction 4.23 5.33 -- 185 2502 0.122 0.1507 -- 99.44
X Ray Diffraction 5.33 41.93 -- 134 2548 0.1299 0.1529 -- 98.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 71.29
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.3558
f_bond_d 0.0024
f_plane_restr 0.0036
f_chiral_restr 0.0467
f_angle_d 0.5697
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3454
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 52

Software

Software
Software Name Purpose
PHENIX refinement version: 1.13_2998
HKL-3000 data reduction
HKL-3000 data scaling
HKL-3000 phasing
MOLREP phasing