X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details HEPES, PEG 4000, NaOAc

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.64 α = 90
b = 115.85 β = 101.35
c = 66.09 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2014-01-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.920 PETRA III, EMBL c/o DESY P13 (MX1)

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
1.53 50 98.5 -- -- -- 4.2 -- 121606 -- -- 20.75
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)
1.53 1.63 98.4 0.496 -- 2.79 -- --

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 1.53 43.185 -- 1.34 -- 121558 6079 98.57 -- 0.1646 0.1634 0.1879 --
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 1.53 1.5474 -- 200 3777 0.2482 0.3021 -- 96.0
X Ray Diffraction 1.5474 1.5656 -- 199 3777 0.255 0.2676 -- 99.0
X Ray Diffraction 1.5656 1.5847 -- 205 3903 0.2434 0.2812 -- 99.0
X Ray Diffraction 1.5847 1.6047 -- 202 3823 0.23 0.2659 -- 99.0
X Ray Diffraction 1.6047 1.6259 -- 204 3883 0.2278 0.2486 -- 99.0
X Ray Diffraction 1.6259 1.6481 -- 203 3864 0.2216 0.2443 -- 99.0
X Ray Diffraction 1.6481 1.6717 -- 202 3828 0.2188 0.234 -- 99.0
X Ray Diffraction 1.6717 1.6966 -- 205 3905 0.2056 0.2646 -- 99.0
X Ray Diffraction 1.6966 1.7231 -- 204 3857 0.1998 0.2322 -- 99.0
X Ray Diffraction 1.7231 1.7514 -- 201 3830 0.1921 0.2302 -- 99.0
X Ray Diffraction 1.7514 1.7816 -- 203 3862 0.1783 0.2118 -- 99.0
X Ray Diffraction 1.7816 1.814 -- 201 3802 0.172 0.2039 -- 98.0
X Ray Diffraction 1.814 1.8489 -- 196 3750 0.1596 0.187 -- 96.0
X Ray Diffraction 1.8489 1.8866 -- 202 3842 0.1631 0.2075 -- 99.0
X Ray Diffraction 1.8866 1.9277 -- 205 3882 0.172 0.2055 -- 99.0
X Ray Diffraction 1.9277 1.9725 -- 202 3846 0.1679 0.2 -- 99.0
X Ray Diffraction 1.9725 2.0218 -- 203 3856 0.1615 0.1957 -- 99.0
X Ray Diffraction 2.0218 2.0765 -- 205 3891 0.1591 0.1938 -- 99.0
X Ray Diffraction 2.0765 2.1376 -- 205 3893 0.1579 0.18 -- 99.0
X Ray Diffraction 2.1376 2.2066 -- 201 3824 0.1526 0.1867 -- 98.0
X Ray Diffraction 2.2066 2.2854 -- 202 3834 0.1535 0.1775 -- 98.0
X Ray Diffraction 2.2854 2.3769 -- 196 3721 0.1463 0.1605 -- 96.0
X Ray Diffraction 2.3769 2.4851 -- 205 3893 0.1542 0.1755 -- 99.0
X Ray Diffraction 2.4851 2.6161 -- 204 3879 0.1616 0.2042 -- 99.0
X Ray Diffraction 2.6161 2.78 -- 206 3908 0.1676 0.1683 -- 99.0
X Ray Diffraction 2.78 2.9946 -- 203 3869 0.1621 0.2151 -- 99.0
X Ray Diffraction 2.9946 3.2958 -- 204 3861 0.1537 0.1826 -- 98.0
X Ray Diffraction 3.2958 3.7725 -- 201 3815 0.146 0.1658 -- 97.0
X Ray Diffraction 3.7725 4.752 -- 206 3926 0.1385 0.1423 -- 100.0
X Ray Diffraction 4.752 43.2026 -- 204 3878 0.1775 0.2014 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.8439
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.873
f_bond_d 0.02
f_chiral_restr 0.107
f_plane_restr 0.01
f_dihedral_angle_d 14.928
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5323
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 653

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling version: 2.5.2
X-PLOR model building
PDB_EXTRACT data extraction version: 3.14
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.9_1690)
XSCALE data reduction