X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 277.0
Details 200 mM potassium acetate, 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.47 α = 90
b = 115.49 β = 90
c = 116.17 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
CCD MARMOSAIC 300 mm CCD -- 2012-12-16
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID

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
1.9 50 99.8 0.102 -- -- 3.9 43956 43868 1.0 1.0 18.75
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)
1.9 1.97 100.0 0.551 -- 2.4 3.9 4308

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 1.9 38.216 -- 1.35 43956 43811 2204 99.84 -- 0.1558 0.1544 0.1817 RANDOM
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 1.9 1.9416 -- 121 2577 0.2039 0.2648 -- 99.0
X Ray Diffraction 1.9416 1.9867 -- 139 2547 0.1942 0.2563 -- 100.0
X Ray Diffraction 1.9867 2.0364 -- 130 2581 0.1923 0.2177 -- 100.0
X Ray Diffraction 2.0364 2.0915 -- 140 2523 0.1699 0.2268 -- 100.0
X Ray Diffraction 2.0915 2.153 -- 136 2598 0.1662 0.1999 -- 100.0
X Ray Diffraction 2.153 2.2225 -- 122 2574 0.1638 0.1898 -- 100.0
X Ray Diffraction 2.2225 2.3019 -- 145 2547 0.1598 0.2196 -- 100.0
X Ray Diffraction 2.3019 2.3941 -- 137 2611 0.1679 0.197 -- 100.0
X Ray Diffraction 2.3941 2.503 -- 140 2570 0.1631 0.2321 -- 100.0
X Ray Diffraction 2.503 2.6349 -- 139 2568 0.16 0.1786 -- 100.0
X Ray Diffraction 2.6349 2.8 -- 134 2608 0.1615 0.184 -- 100.0
X Ray Diffraction 2.8 3.0161 -- 137 2609 0.1649 0.1875 -- 100.0
X Ray Diffraction 3.0161 3.3195 -- 127 2651 0.1399 0.1812 -- 100.0
X Ray Diffraction 3.3195 3.7994 -- 148 2607 0.1302 0.1426 -- 100.0
X Ray Diffraction 3.7994 4.7854 -- 155 2657 0.1249 0.1485 -- 100.0
X Ray Diffraction 4.7854 38.2235 -- 154 2779 0.1571 0.1566 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.7509
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.12
f_plane_restr 0.005
f_chiral_restr 0.078
f_angle_d 1.299
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2954
Nucleic Acid Atoms 818
Heterogen Atoms 65
Solvent Atoms 698

Software

Computing
Computing Package Purpose
SER-gui Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.1_1168) Structure Solution
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