X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 100 mM Tris-HCl, 150 mM magnesium chloride hexahydrate, 25% PEG4000, 6% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.82 α = 90
b = 151.09 β = 90
c = 170.34 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
PIXEL DECTRIS PILATUS 6M Rh coated mirror, K-B focusing mirror 2013-02-17
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.00 SSRL BL12-2

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
3 38.7 98.9 -- -- -- 6.5 -- 44496 -- -- --
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)
3.0 3.17 94.3 -- -- -- 6.0 --

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 3.003 38.695 -- 1.34 -- 43862 2202 97.54 -- 0.1944 0.1909 0.2605 --
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 3.003 3.0683 -- 108 1823 0.3901 0.4493 -- 70.0
X Ray Diffraction 3.0683 3.1396 -- 124 2620 0.2804 0.3146 -- 100.0
X Ray Diffraction 3.1396 3.2181 -- 137 2640 0.2639 0.374 -- 100.0
X Ray Diffraction 3.2181 3.3051 -- 137 2626 0.2411 0.3184 -- 100.0
X Ray Diffraction 3.3051 3.4023 -- 140 2614 0.212 0.3336 -- 99.0
X Ray Diffraction 3.4023 3.512 -- 144 2600 0.2158 0.2603 -- 99.0
X Ray Diffraction 3.512 3.6375 -- 130 2618 0.1998 0.2482 -- 99.0
X Ray Diffraction 3.6375 3.783 -- 149 2658 0.2044 0.3066 -- 100.0
X Ray Diffraction 3.783 3.955 -- 131 2622 0.1897 0.2692 -- 99.0
X Ray Diffraction 3.955 4.1633 -- 146 2633 0.1876 0.2743 -- 100.0
X Ray Diffraction 4.1633 4.4238 -- 129 2647 0.174 0.2466 -- 99.0
X Ray Diffraction 4.4238 4.7648 -- 141 2690 0.153 0.213 -- 99.0
X Ray Diffraction 4.7648 5.2432 -- 111 2681 0.1589 0.2137 -- 100.0
X Ray Diffraction 5.2432 5.9995 -- 164 2669 0.1859 0.2521 -- 99.0
X Ray Diffraction 5.9995 7.5495 -- 148 2723 0.1913 0.2568 -- 100.0
X Ray Diffraction 7.5495 38.6983 -- 163 2796 0.1588 0.2122 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.778
f_plane_restr 0.009
f_chiral_restr 0.056
f_bond_d 0.01
f_angle_d 1.328
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14797
Nucleic Acid Atoms 0
Heterogen Atoms 268
Solvent Atoms 8

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
XDS data reduction
SCALA data scaling