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 = 54.58 α = 90
b = 79.13 β = 105.95
c = 54.98 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 2013-07-10
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
2.04 14 99.2 0.089 -- -- 6.9 -- n/a -- -- 31.15
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)
2.04 2.11 92.4 0.593 -- -- 4.4 2633

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 2.038 13.984 -- 1.34 -- 55412 5574 98.41 -- 0.1909 0.1864 0.2299 --
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 2.0379 2.061 -- 127 1168 0.4278 0.4869 -- 70.0
X Ray Diffraction 2.061 2.0851 -- 164 1548 0.2987 0.3551 -- 91.0
X Ray Diffraction 2.0851 2.1105 -- 219 1574 0.2674 0.2945 -- 95.0
X Ray Diffraction 2.1105 2.1371 -- 194 1659 0.266 0.284 -- 98.0
X Ray Diffraction 2.1371 2.1651 -- 200 1603 0.2702 0.3355 -- 100.0
X Ray Diffraction 2.1651 2.1947 -- 210 1730 0.2545 0.2908 -- 100.0
X Ray Diffraction 2.1947 2.2259 -- 167 1635 0.2328 0.3249 -- 100.0
X Ray Diffraction 2.2259 2.259 -- 201 1736 0.2316 0.2892 -- 100.0
X Ray Diffraction 2.259 2.2941 -- 201 1697 0.2167 0.2452 -- 100.0
X Ray Diffraction 2.2941 2.3316 -- 160 1648 0.2185 0.2503 -- 100.0
X Ray Diffraction 2.3316 2.3716 -- 209 1686 0.211 0.2827 -- 100.0
X Ray Diffraction 2.3716 2.4145 -- 152 1734 0.2106 0.28 -- 100.0
X Ray Diffraction 2.4145 2.4607 -- 195 1715 0.2096 0.2597 -- 100.0
X Ray Diffraction 2.4607 2.5107 -- 161 1697 0.1983 0.2895 -- 100.0
X Ray Diffraction 2.5107 2.5649 -- 190 1684 0.2003 0.2375 -- 100.0
X Ray Diffraction 2.5649 2.6242 -- 200 1676 0.1975 0.2877 -- 100.0
X Ray Diffraction 2.6242 2.6894 -- 176 1674 0.1909 0.2749 -- 100.0
X Ray Diffraction 2.6894 2.7616 -- 218 1683 0.2023 0.2874 -- 100.0
X Ray Diffraction 2.7616 2.8422 -- 190 1680 0.2012 0.326 -- 100.0
X Ray Diffraction 2.8422 2.9331 -- 162 1719 0.2006 0.2346 -- 100.0
X Ray Diffraction 2.9331 3.0369 -- 171 1732 0.2084 0.2597 -- 100.0
X Ray Diffraction 3.0369 3.1571 -- 196 1636 0.1978 0.2644 -- 100.0
X Ray Diffraction 3.1571 3.299 -- 206 1700 0.1789 0.2531 -- 100.0
X Ray Diffraction 3.299 3.4705 -- 157 1724 0.1636 0.1931 -- 100.0
X Ray Diffraction 3.4705 3.6842 -- 188 1702 0.1522 0.1709 -- 100.0
X Ray Diffraction 3.6842 3.9626 -- 202 1657 0.1501 0.1717 -- 100.0
X Ray Diffraction 3.9626 4.3505 -- 201 1686 0.1452 0.1646 -- 100.0
X Ray Diffraction 4.3505 4.9553 -- 165 1711 0.1482 0.1836 -- 100.0
X Ray Diffraction 4.9553 6.1533 -- 167 1699 0.1695 0.1935 -- 100.0
X Ray Diffraction 6.1533 13.9843 -- 225 1645 0.1703 0.1924 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.336
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.319
f_plane_restr 0.002
f_chiral_restr 0.042
f_angle_d 0.707
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2404
Nucleic Acid Atoms 627
Heterogen Atoms 33
Solvent Atoms 339

Software

Computing
Computing Package Purpose
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