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_angle_d 0.707
f_bond_d 0.002
f_plane_restr 0.002
f_chiral_restr 0.042
f_dihedral_angle_d 18.319
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11