X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 0.1 M CHES pH 9.5, 0.1 M magnesium acetate, and 17% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.29 α = 90
b = 142.9 β = 90
c = 151.16 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2019-07-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C

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
2.09 151.16 99.5 0.081 -- -- 6.6 -- 67360 -- -- 43.77
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)
2.09 2.14 94.1 1.305 -- 1.4 6.6 --

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 2.09 103.84 -- 0.31 -- 67244 3269 99.44 -- 0.2065 0.2052 0.233 --
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 2.09 2.13 -- 145 2456 0.307 0.3228 -- 90.25
X Ray Diffraction 2.13 2.16 -- 146 2757 0.2802 0.32 -- 99.97
X Ray Diffraction 2.16 2.19 -- 128 2764 0.2698 0.2616 -- 99.9
X Ray Diffraction 2.19 2.23 -- 145 2734 0.265 0.3193 -- 99.76
X Ray Diffraction 2.23 2.27 -- 158 2781 0.2505 0.2985 -- 99.97
X Ray Diffraction 2.27 2.32 -- 144 2705 0.2433 0.2963 -- 99.82
X Ray Diffraction 2.32 2.36 -- 160 2785 0.2305 0.2626 -- 100.0
X Ray Diffraction 2.36 2.42 -- 132 2764 0.2274 0.2484 -- 99.9
X Ray Diffraction 2.42 2.47 -- 140 2738 0.221 0.2621 -- 99.72
X Ray Diffraction 2.47 2.53 -- 141 2779 0.2253 0.2251 -- 99.79
X Ray Diffraction 2.53 2.6 -- 165 2759 0.2265 0.2978 -- 99.97
X Ray Diffraction 2.6 2.68 -- 131 2751 0.2379 0.3116 -- 99.9
X Ray Diffraction 2.68 2.76 -- 154 2811 0.2292 0.2874 -- 99.93
X Ray Diffraction 2.76 2.86 -- 136 2767 0.2199 0.2331 -- 99.93
X Ray Diffraction 2.86 2.98 -- 141 2788 0.2249 0.2589 -- 99.97
X Ray Diffraction 2.98 3.11 -- 140 2790 0.2256 0.2835 -- 99.93
X Ray Diffraction 3.11 3.28 -- 149 2807 0.2236 0.2873 -- 99.73
X Ray Diffraction 3.28 3.48 -- 113 2840 0.207 0.2371 -- 99.93
X Ray Diffraction 3.48 3.75 -- 127 2824 0.19 0.2124 -- 99.9
X Ray Diffraction 3.75 4.13 -- 140 2812 0.1736 0.1702 -- 99.8
X Ray Diffraction 4.13 4.73 -- 140 2872 0.1591 0.1805 -- 99.8
X Ray Diffraction 4.73 5.96 -- 123 2898 0.1855 0.1947 -- 99.83
X Ray Diffraction 5.96 103.84 -- 171 2993 0.2006 0.2121 -- 99.31
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.52
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.0396
f_angle_d 0.6283
f_plane_restr 0.0038
f_bond_d 0.0026
f_dihedral_angle_d 12.3413
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7805
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 383

Software

Software
Software Name Purpose
PHENIX refinement version: 1.16_3549
PHENIX refinement version: 1.16_3549
XDS data reduction
Aimless data scaling
PHASER phasing