X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details potassium cacodylate, potassium chloride, manganese chloride

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.18 α = 90
b = 105.82 β = 90
c = 166.26 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 2M-F -- 2014-11-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A

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
2.35 50 99.4 0.1 -- 25.577 7.4 -- 72824 -- -- 40.83
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)
2.35 2.43 98.5 0.299 -- -- 5.7 --

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 2.35 49.091 -- 1.44 -- 72359 3645 99.4 -- 0.2283 0.2266 0.2593 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 2.35 2.3809 -- 125 2584 0.2797 0.3062 -- 98.0
X Ray Diffraction 2.3809 2.4135 -- 129 2605 0.2744 0.3216 -- 99.0
X Ray Diffraction 2.4135 2.448 -- 150 2595 0.2819 0.3057 -- 99.0
X Ray Diffraction 2.448 2.4846 -- 162 2533 0.2743 0.2908 -- 98.0
X Ray Diffraction 2.4846 2.5234 -- 130 2611 0.271 0.3266 -- 98.0
X Ray Diffraction 2.5234 2.5647 -- 148 2564 0.2722 0.2883 -- 99.0
X Ray Diffraction 2.5647 2.609 -- 115 2613 0.2612 0.3113 -- 99.0
X Ray Diffraction 2.609 2.6564 -- 141 2630 0.2671 0.3107 -- 99.0
X Ray Diffraction 2.6564 2.7075 -- 147 2597 0.2693 0.3437 -- 99.0
X Ray Diffraction 2.7075 2.7628 -- 130 2612 0.2705 0.2797 -- 99.0
X Ray Diffraction 2.7628 2.8228 -- 122 2666 0.2574 0.2952 -- 100.0
X Ray Diffraction 2.8228 2.8885 -- 137 2639 0.2551 0.3001 -- 100.0
X Ray Diffraction 2.8885 2.9607 -- 134 2613 0.2653 0.2685 -- 100.0
X Ray Diffraction 2.9607 3.0407 -- 124 2629 0.269 0.2941 -- 100.0
X Ray Diffraction 3.0407 3.1302 -- 148 2660 0.2656 0.3401 -- 100.0
X Ray Diffraction 3.1302 3.2312 -- 125 2647 0.2613 0.3078 -- 100.0
X Ray Diffraction 3.2312 3.3467 -- 145 2641 0.2367 0.272 -- 100.0
X Ray Diffraction 3.3467 3.4806 -- 153 2646 0.2282 0.2552 -- 100.0
X Ray Diffraction 3.4806 3.639 -- 161 2640 0.2189 0.2734 -- 100.0
X Ray Diffraction 3.639 3.8308 -- 143 2642 0.2235 0.2443 -- 100.0
X Ray Diffraction 3.8308 4.0707 -- 153 2676 0.208 0.2589 -- 100.0
X Ray Diffraction 4.0707 4.3848 -- 151 2669 0.1965 0.2202 -- 100.0
X Ray Diffraction 4.3848 4.8257 -- 133 2702 0.1943 0.2343 -- 100.0
X Ray Diffraction 4.8257 5.5232 -- 160 2691 0.2037 0.2147 -- 100.0
X Ray Diffraction 5.5232 6.9555 -- 128 2757 0.2153 0.2324 -- 100.0
X Ray Diffraction 6.9555 49.1017 -- 151 2852 0.1719 0.1953 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.5463
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.024
f_dihedral_angle_d 26.806
f_plane_restr 0.002
f_bond_d 0.003
f_angle_d 0.579
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5940
Nucleic Acid Atoms 5980
Heterogen Atoms 14
Solvent Atoms 88

Software

Software
Software Name Purpose
HKL-2000 data scaling version: 706
PHASER phasing version: 2.5.6
PHENIX refinement version: 1.9_1692
PDB_EXTRACT data extraction version: 3.20