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 = 99.64 α = 90
b = 108.77 β = 90
c = 171.14 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 PILATUS3 6M -- 2014-10-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU

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
2.55 50 98.4 0.1 -- 28.5 8.4 -- 59824 -- -- 47.28
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)
2.55 2.64 91.3 0.353 -- -- 3.8 5459

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 2.557 49.817 -- 1.43 -- 59767 3021 98.23 -- 0.2123 0.2103 0.2488 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 2.5572 2.5971 -- 113 2214 0.2686 0.3375 -- 84.0
X Ray Diffraction 2.5971 2.6397 -- 126 2402 0.2802 0.3087 -- 93.0
X Ray Diffraction 2.6397 2.6852 -- 118 2543 0.283 0.3356 -- 97.0
X Ray Diffraction 2.6852 2.734 -- 134 2528 0.2649 0.3443 -- 98.0
X Ray Diffraction 2.734 2.7866 -- 122 2573 0.2634 0.2918 -- 99.0
X Ray Diffraction 2.7866 2.8435 -- 131 2571 0.2558 0.3333 -- 99.0
X Ray Diffraction 2.8435 2.9053 -- 150 2527 0.2534 0.3003 -- 99.0
X Ray Diffraction 2.9053 2.9729 -- 144 2560 0.2529 0.2557 -- 99.0
X Ray Diffraction 2.9729 3.0472 -- 130 2586 0.2646 0.3506 -- 99.0
X Ray Diffraction 3.0472 3.1296 -- 136 2596 0.2505 0.3297 -- 99.0
X Ray Diffraction 3.1296 3.2217 -- 135 2577 0.247 0.328 -- 99.0
X Ray Diffraction 3.2217 3.3257 -- 136 2586 0.2457 0.2639 -- 99.0
X Ray Diffraction 3.3257 3.4445 -- 123 2618 0.2327 0.2878 -- 100.0
X Ray Diffraction 3.4445 3.5824 -- 130 2611 0.22 0.2455 -- 100.0
X Ray Diffraction 3.5824 3.7453 -- 158 2601 0.2162 0.2558 -- 100.0
X Ray Diffraction 3.7453 3.9427 -- 139 2595 0.2027 0.253 -- 100.0
X Ray Diffraction 3.9427 4.1896 -- 152 2650 0.1897 0.2525 -- 100.0
X Ray Diffraction 4.1896 4.5129 -- 146 2629 0.181 0.1959 -- 100.0
X Ray Diffraction 4.5129 4.9667 -- 152 2626 0.1746 0.2347 -- 100.0
X Ray Diffraction 4.9667 5.6845 -- 155 2655 0.1829 0.2183 -- 100.0
X Ray Diffraction 5.6845 7.1585 -- 138 2688 0.2 0.2424 -- 100.0
X Ray Diffraction 7.1585 49.8269 -- 153 2810 0.1598 0.166 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.0352
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.052
f_plane_restr 0.006
f_dihedral_angle_d 26.494
f_bond_d 0.009
f_angle_d 1.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5971
Nucleic Acid Atoms 5980
Heterogen Atoms 10
Solvent Atoms 32

Software

Software
Software Name Purpose
HKL-2000 data collection
HKL-2000 data scaling
PHENIX refinement version: (phenix.refine: 1.9_1692)
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction version: 705b
PHASER phasing version: 2.5.1