X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 400 nl of protein + 400 nl of Morpheus condition C4 - 0.1 M MES/imidazole pH 6.5, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.83 α = 90
b = 70.02 β = 90
c = 140.01 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-04-29
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1

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
1.6 50 99.4 0.047 -- -- 5.84 -- 40085 -- -3.0 14.78
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)
1.6 1.64 93.4 0.402 -- 3.24 3.86 --

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
-- 1.603 46.347 -- 1.38 -- 40044 2024 99.37 -- 0.1557 0.1539 0.1901 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 1.603 1.6426 -- 119 2501 0.2108 0.2633 -- 93.0
X Ray Diffraction 1.6426 1.687 -- 159 2695 0.1858 0.2197 -- 100.0
X Ray Diffraction 1.687 1.7367 -- 151 2713 0.162 0.2026 -- 100.0
X Ray Diffraction 1.7367 1.7927 -- 160 2688 0.1579 0.2041 -- 100.0
X Ray Diffraction 1.7927 1.8568 -- 156 2680 0.1575 0.2045 -- 100.0
X Ray Diffraction 1.8568 1.9311 -- 143 2709 0.1538 0.1986 -- 100.0
X Ray Diffraction 1.9311 2.019 -- 151 2711 0.1542 0.1983 -- 100.0
X Ray Diffraction 2.019 2.1255 -- 123 2743 0.1484 0.1992 -- 100.0
X Ray Diffraction 2.1255 2.2586 -- 138 2705 0.1456 0.1957 -- 100.0
X Ray Diffraction 2.2586 2.433 -- 134 2759 0.1556 0.1867 -- 100.0
X Ray Diffraction 2.433 2.6778 -- 130 2757 0.1601 0.1642 -- 100.0
X Ray Diffraction 2.6778 3.0652 -- 151 2742 0.1605 0.1804 -- 100.0
X Ray Diffraction 3.0652 3.8616 -- 157 2768 0.1457 0.1797 -- 100.0
X Ray Diffraction 3.8616 46.3662 -- 152 2849 0.1438 0.1881 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.693
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.288
f_chiral_restr 0.056
f_plane_restr 0.006
f_bond_d 0.009
f_dihedral_angle_d 13.446
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 0
Solvent Atoms 349

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHASER phasing
PDB_EXTRACT data extraction version: 3.14
PHENIX refinement version: (phenix.refine: 1.9_1692)