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 = 105.55 α = 90
b = 109.38 β = 90
c = 176.21 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 -- 2013-05-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 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
3.45 50 99.3 0.097 -- -- 5.9 -- 28747 -- -- 91.24
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)
3.45 3.57 98.9 0.426 -- -- 5.8 2815

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 3.45 34.875 -- 0.16 -- 26553 1902 96.54 -- 0.2037 0.1997 0.2544 --
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 3.4501 3.5363 -- 122 1623 0.2528 0.3182 0.0 90.0
X Ray Diffraction 3.5363 3.6319 -- 123 1651 0.2271 0.298 0.0 92.0
X Ray Diffraction 3.6319 3.7386 -- 138 1656 0.2376 0.3165 0.0 93.0
X Ray Diffraction 3.7386 3.8591 -- 130 1699 0.2321 0.2951 0.0 95.0
X Ray Diffraction 3.8591 3.9969 -- 136 1727 0.2212 0.3046 0.0 95.0
X Ray Diffraction 3.9969 4.1567 -- 135 1721 0.2114 0.2672 0.0 96.0
X Ray Diffraction 4.1567 4.3455 -- 130 1765 0.1999 0.2602 0.0 97.0
X Ray Diffraction 4.3455 4.5741 -- 142 1781 0.1929 0.2526 0.0 98.0
X Ray Diffraction 4.5741 4.86 -- 130 1787 0.1867 0.2377 0.0 99.0
X Ray Diffraction 4.86 5.2341 -- 139 1805 0.1937 0.2461 0.0 99.0
X Ray Diffraction 5.2341 5.7587 -- 145 1804 0.2095 0.2571 0.0 99.0
X Ray Diffraction 5.7587 6.5871 -- 142 1846 0.2221 0.2882 0.0 100.0
X Ray Diffraction 6.5871 8.2807 -- 140 1850 0.1843 0.2284 0.0 99.0
X Ray Diffraction 8.2807 34.8765 -- 150 1936 0.1713 0.208 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 112.23
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.247
f_bond_d 0.011
f_chiral_restr 0.061
f_dihedral_angle_d 26.901
f_plane_restr 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5940
Nucleic Acid Atoms 5980
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
HKL-2000 data scaling version: 704w
PHASER phasing version: 2.5.1
PDB_EXTRACT data extraction version: 3.22
HKL data scaling