X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 291.0
Details 50mM Na-Cacodylate, 20mM MgCl2, 1mM Cobalt(III)-hexamminechloride, 1mM Spermine, 20%v/v 2-propanol, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 144.87 α = 90
b = 111.78 β = 90
c = 67.1 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M LN2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror 2012-06-28
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.00002 SLS X06SA

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
2.29 49.32 99.7 0.135 0.131 -- 16.15 49885 49755 0.0 1.81 43.91
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)
2.29 2.35 96.7 1.888 1.965 1.81 13.16 3506

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 2.29 45.05 -- 2.0 49755 49743 2516 99.74 0.1827 0.1827 0.1807 0.2184 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 2.2895 2.3335 -- 135 2482 0.3126 0.3623 -- 96.0
X Ray Diffraction 2.3335 2.3812 -- 135 2574 0.2618 0.3336 -- 100.0
X Ray Diffraction 2.3812 2.4329 -- 132 2607 0.2299 0.2692 -- 100.0
X Ray Diffraction 2.4329 2.4895 -- 134 2601 0.2203 0.2446 -- 100.0
X Ray Diffraction 2.4895 2.5518 -- 149 2561 0.2144 0.2659 -- 100.0
X Ray Diffraction 2.5518 2.6208 -- 120 2619 0.2074 0.2623 -- 100.0
X Ray Diffraction 2.6208 2.6979 -- 144 2610 0.2095 0.2662 -- 100.0
X Ray Diffraction 2.6979 2.785 -- 150 2607 0.2078 0.257 -- 100.0
X Ray Diffraction 2.785 2.8845 -- 138 2575 0.2028 0.2529 -- 100.0
X Ray Diffraction 2.8845 2.9999 -- 132 2630 0.203 0.239 -- 100.0
X Ray Diffraction 2.9999 3.1364 -- 127 2628 0.2042 0.2328 -- 100.0
X Ray Diffraction 3.1364 3.3018 -- 149 2616 0.1982 0.2506 -- 100.0
X Ray Diffraction 3.3018 3.5086 -- 145 2622 0.1865 0.2747 -- 100.0
X Ray Diffraction 3.5086 3.7793 -- 144 2639 0.175 0.2271 -- 100.0
X Ray Diffraction 3.7793 4.1594 -- 130 2671 0.1582 0.1792 -- 100.0
X Ray Diffraction 4.1594 4.7607 -- 153 2652 0.139 0.1742 -- 100.0
X Ray Diffraction 4.7607 5.9958 -- 151 2691 0.1605 0.194 -- 100.0
X Ray Diffraction 5.9958 45.0589 -- 148 2842 0.1611 0.1696 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.8922
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.051
f_dihedral_angle_d 15.254
f_angle_d 0.72
f_bond_d 0.003
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6209
Nucleic Acid Atoms 529
Heterogen Atoms 16
Solvent Atoms 367

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XDS/XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: dev_1243) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1243) refinement
PHENIX model building
XDS data collection