X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.42 α = 90
b = 79.42 β = 105.25
c = 54.81 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 104
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors 2013-05-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.01 14 97.4 0.081 -- -- 6.8 -- n/a -- -- 27.53
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)
2.01 2.08 94.1 0.674 -- -- 4.5 2772

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
Isomorphous replacement 2.01 13.701 -- 1.34 -- 56743 5711 96.59 -- 0.1897 0.1858 0.2237 --
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 2.0098 2.0326 -- 156 1451 0.314 0.3687 -- 83.0
X Ray Diffraction 2.0326 2.0564 -- 170 1523 0.2911 0.2714 -- 89.0
X Ray Diffraction 2.0564 2.0814 -- 181 1665 0.2801 0.3097 -- 92.0
X Ray Diffraction 2.0814 2.1077 -- 220 1639 0.2598 0.285 -- 94.0
X Ray Diffraction 2.1077 2.1353 -- 195 1637 0.2602 0.2961 -- 95.0
X Ray Diffraction 2.1353 2.1644 -- 200 1685 0.2479 0.3055 -- 95.0
X Ray Diffraction 2.1644 2.1952 -- 203 1688 0.2398 0.2749 -- 96.0
X Ray Diffraction 2.1952 2.2279 -- 181 1654 0.2341 0.2552 -- 96.0
X Ray Diffraction 2.2279 2.2625 -- 195 1722 0.2158 0.2534 -- 96.0
X Ray Diffraction 2.2625 2.2995 -- 205 1705 0.2174 0.2629 -- 97.0
X Ray Diffraction 2.2995 2.3389 -- 179 1676 0.2173 0.2353 -- 96.0
X Ray Diffraction 2.3389 2.3812 -- 194 1726 0.1961 0.2653 -- 97.0
X Ray Diffraction 2.3812 2.4268 -- 164 1695 0.198 0.2521 -- 97.0
X Ray Diffraction 2.4268 2.476 -- 184 1788 0.2009 0.2344 -- 97.0
X Ray Diffraction 2.476 2.5296 -- 183 1680 0.1923 0.247 -- 97.0
X Ray Diffraction 2.5296 2.588 -- 194 1725 0.1967 0.2506 -- 98.0
X Ray Diffraction 2.588 2.6523 -- 195 1712 0.1985 0.2408 -- 97.0
X Ray Diffraction 2.6523 2.7235 -- 211 1717 0.1963 0.2568 -- 98.0
X Ray Diffraction 2.7235 2.8029 -- 224 1690 0.1941 0.2277 -- 98.0
X Ray Diffraction 2.8029 2.8926 -- 146 1782 0.1924 0.2521 -- 98.0
X Ray Diffraction 2.8926 2.9949 -- 170 1765 0.1997 0.2579 -- 98.0
X Ray Diffraction 2.9949 3.1135 -- 185 1735 0.2014 0.2405 -- 98.0
X Ray Diffraction 3.1135 3.2534 -- 217 1701 0.1868 0.2253 -- 99.0
X Ray Diffraction 3.2534 3.4224 -- 176 1765 0.1679 0.2258 -- 99.0
X Ray Diffraction 3.4224 3.6331 -- 177 1777 0.1663 0.2129 -- 99.0
X Ray Diffraction 3.6331 3.9076 -- 229 1708 0.153 0.1845 -- 99.0
X Ray Diffraction 3.9076 4.2898 -- 184 1723 0.1485 0.1851 -- 99.0
X Ray Diffraction 4.2898 4.8857 -- 179 1798 0.1418 0.1657 -- 100.0
X Ray Diffraction 4.8857 6.0653 -- 181 1789 0.1642 0.2068 -- 100.0
X Ray Diffraction 6.0653 13.7009 -- 233 1711 0.1581 0.1716 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.4245
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.129
f_plane_restr 0.003
f_chiral_restr 0.045
f_angle_d 0.763
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2443
Nucleic Acid Atoms 627
Heterogen Atoms 3
Solvent Atoms 354

Software

Computing
Computing Package Purpose
Mar Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection