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 = 99.49 α = 90
b = 108.77 β = 90
c = 169.57 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 -- 2015-12-15
Diffraction Radiation
Monochromator Protocol
Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooled. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A

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
2.5 50 99.8 0.093 -- 17.5 9.2 -- 64545 -- -- 42.19
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)
2.5 2.59 99.8 0.418 -- -- 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 2.5 49.146 -- 1.44 -- 64243 3290 99.86 -- 0.1956 0.1929 0.2454 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 2.5 2.5373 -- 129 2604 0.2196 0.2708 -- 100.0
X Ray Diffraction 2.5373 2.577 -- 152 2611 0.237 0.3055 -- 100.0
X Ray Diffraction 2.577 2.6192 -- 147 2624 0.248 0.3351 -- 100.0
X Ray Diffraction 2.6192 2.6644 -- 126 2608 0.2442 0.3092 -- 100.0
X Ray Diffraction 2.6644 2.7128 -- 150 2590 0.2512 0.2933 -- 100.0
X Ray Diffraction 2.7128 2.765 -- 132 2647 0.2429 0.3141 -- 100.0
X Ray Diffraction 2.765 2.8214 -- 152 2594 0.2405 0.3191 -- 100.0
X Ray Diffraction 2.8214 2.8828 -- 135 2654 0.2261 0.3206 -- 100.0
X Ray Diffraction 2.8828 2.9498 -- 146 2610 0.2289 0.2731 -- 100.0
X Ray Diffraction 2.9498 3.0236 -- 147 2631 0.2316 0.2818 -- 100.0
X Ray Diffraction 3.0236 3.1053 -- 138 2631 0.2257 0.2838 -- 100.0
X Ray Diffraction 3.1053 3.1967 -- 136 2643 0.2097 0.2611 -- 100.0
X Ray Diffraction 3.1967 3.2998 -- 147 2623 0.1995 0.2613 -- 100.0
X Ray Diffraction 3.2998 3.4178 -- 148 2632 0.1958 0.2359 -- 100.0
X Ray Diffraction 3.4178 3.5546 -- 142 2637 0.1928 0.2721 -- 100.0
X Ray Diffraction 3.5546 3.7163 -- 147 2645 0.1991 0.2547 -- 100.0
X Ray Diffraction 3.7163 3.9121 -- 146 2659 0.1925 0.2595 -- 100.0
X Ray Diffraction 3.9121 4.1571 -- 148 2658 0.171 0.2142 -- 100.0
X Ray Diffraction 4.1571 4.4779 -- 127 2689 0.1657 0.2181 -- 100.0
X Ray Diffraction 4.4779 4.9281 -- 135 2699 0.1663 0.2177 -- 100.0
X Ray Diffraction 4.9281 5.6404 -- 139 2700 0.1727 0.1956 -- 100.0
X Ray Diffraction 5.6404 7.1029 -- 153 2727 0.1875 0.2186 -- 100.0
X Ray Diffraction 7.1029 49.1555 -- 168 2837 0.1516 0.1951 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.7851
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.059
f_plane_restr 0.007
f_dihedral_angle_d 29.12
f_bond_d 0.012
f_angle_d 1.279
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6119
Nucleic Acid Atoms 5900
Heterogen Atoms 19
Solvent Atoms 244

Software

Software
Software Name Purpose
HKL-2000 data scaling
PHENIX refinement version: 1.9_1692
PDB_EXTRACT data extraction version: 3.20
Coot model building
PHASER phasing