X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 20% PEG3350, 0.2M magnesium formate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.82 α = 90
b = 108.82 β = 90
c = 57.93 γ = 90
Symmetry
Space Group I 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2017-09-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03

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
1.52 54.41 100.0 0.051 -- -- 6.4 -- 52114 -- -- --
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)
1.52 1.56 99.9 1.55 -- -- 6.3 --

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 1.52 54.412 -- 1.34 -- 51629 2627 98.99 -- 0.1759 0.1751 0.1904 --
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 1.5198 1.5474 -- 146 2446 0.3314 0.3383 0.0 96.0
X Ray Diffraction 1.5474 1.5772 -- 125 2541 0.3101 0.3901 0.0 97.0
X Ray Diffraction 1.5772 1.6094 -- 125 2527 0.3036 0.3188 0.0 97.0
X Ray Diffraction 1.6094 1.6444 -- 141 2553 0.2793 0.2684 0.0 98.0
X Ray Diffraction 1.6444 1.6827 -- 117 2545 0.268 0.2772 0.0 98.0
X Ray Diffraction 1.6827 1.7247 -- 133 2546 0.2416 0.2935 0.0 98.0
X Ray Diffraction 1.7247 1.7714 -- 120 2572 0.2247 0.2545 0.0 99.0
X Ray Diffraction 1.7714 1.8235 -- 145 2579 0.209 0.2525 0.0 99.0
X Ray Diffraction 1.8235 1.8824 -- 147 2568 0.2049 0.222 0.0 99.0
X Ray Diffraction 1.8824 1.9496 -- 156 2577 0.1813 0.214 0.0 100.0
X Ray Diffraction 1.9496 2.0277 -- 122 2609 0.1653 0.2155 0.0 100.0
X Ray Diffraction 2.0277 2.12 -- 176 2569 0.1621 0.1924 0.0 100.0
X Ray Diffraction 2.12 2.2318 -- 133 2610 0.1579 0.1722 0.0 100.0
X Ray Diffraction 2.2318 2.3716 -- 138 2599 0.1575 0.2056 0.0 100.0
X Ray Diffraction 2.3716 2.5547 -- 134 2593 0.1662 0.1802 0.0 100.0
X Ray Diffraction 2.5547 2.8118 -- 132 2624 0.1576 0.1826 0.0 100.0
X Ray Diffraction 2.8118 3.2186 -- 148 2623 0.1606 0.1744 0.0 100.0
X Ray Diffraction 3.2186 4.0549 -- 134 2633 0.1508 0.1425 0.0 100.0
X Ray Diffraction 4.0549 54.4474 -- 155 2688 0.162 0.1676 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.0289
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_chiral_restr 0.056
f_angle_d 0.956
f_plane_restr 0.005
f_dihedral_angle_d 10.096
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2305
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 276

Software

Software
Software Name Purpose
PHENIX refinement version: 1.12_2829
XDS data reduction
Aimless data scaling version: 0.5.32
PHASER phasing version: 2.6.1
PDB_EXTRACT data extraction version: 3.24