X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 0.1 M Hepes, 14% PEG 4000, 75 mM NaCl, 5% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.46 α = 90
b = 74.93 β = 96.44
c = 98.67 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-11-21
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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
2.15 19.9 98.8 0.081 -- -- -- -- 38614 -- -3.0 33.527
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)
2.15 2.5 99.4 0.337 -- 3.83 -- --

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 2.15 19.896 -- 2.0 38614 38611 1931 98.95 -- 0.1713 0.1692 0.2109 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 2.15 2.2037 -- 136 2584 0.2132 0.2714 -- 100.0
X Ray Diffraction 2.2037 2.2632 -- 138 2633 0.2035 0.2907 -- 100.0
X Ray Diffraction 2.2632 2.3297 -- 138 2607 0.1993 0.2554 -- 99.0
X Ray Diffraction 2.3297 2.4048 -- 139 2639 0.183 0.2344 -- 100.0
X Ray Diffraction 2.4048 2.4906 -- 138 2625 0.1845 0.2363 -- 99.0
X Ray Diffraction 2.4906 2.5901 -- 138 2618 0.182 0.2598 -- 99.0
X Ray Diffraction 2.5901 2.7077 -- 136 2600 0.1794 0.2437 -- 99.0
X Ray Diffraction 2.7077 2.8501 -- 138 2622 0.1926 0.2527 -- 99.0
X Ray Diffraction 2.8501 3.0281 -- 139 2631 0.187 0.2307 -- 99.0
X Ray Diffraction 3.0281 3.2609 -- 137 2612 0.1848 0.2436 -- 99.0
X Ray Diffraction 3.2609 3.5874 -- 138 2611 0.1631 0.2298 -- 98.0
X Ray Diffraction 3.5874 4.1025 -- 138 2619 0.1442 0.1612 -- 99.0
X Ray Diffraction 4.1025 5.1538 -- 138 2622 0.1304 0.1382 -- 98.0
X Ray Diffraction 5.1538 19.8965 -- 140 2657 0.1638 0.1818 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.7075
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.687
f_plane_restr 0.004
f_chiral_restr 0.06
f_angle_d 0.932
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5086
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 390

Software

Computing
Computing Package Purpose
Locally modified Blu-Ice Gui interface to EPICS control Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction