X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.21 α = 90
b = 108.21 β = 90
c = 90.4 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator 2010-04-22
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 1.00 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
1.79 50 99.5 0.065 -- -- -- 57268 57268 0.0 -3.0 --
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)
1.79 1.9 97.3 0.724 -- 2.01 -- --

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 1.8 46.856 -- 2.01 56899 56899 2857 99.98 -- 0.1567 0.1553 0.1825 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 1.8 1.8311 -- 141 2696 0.2325 0.2887 -- 100.0
X Ray Diffraction 1.8311 1.8644 -- 143 2650 0.2136 0.261 -- 100.0
X Ray Diffraction 1.8644 1.9002 -- 132 2665 0.205 0.2611 -- 100.0
X Ray Diffraction 1.9002 1.939 -- 134 2685 0.1891 0.2301 -- 100.0
X Ray Diffraction 1.939 1.9812 -- 156 2668 0.1732 0.2316 -- 100.0
X Ray Diffraction 1.9812 2.0273 -- 139 2669 0.1723 0.2293 -- 100.0
X Ray Diffraction 2.0273 2.078 -- 167 2679 0.1656 0.2277 -- 100.0
X Ray Diffraction 2.078 2.1342 -- 122 2700 0.1604 0.2084 -- 100.0
X Ray Diffraction 2.1342 2.197 -- 132 2679 0.1528 0.201 -- 100.0
X Ray Diffraction 2.197 2.2679 -- 131 2718 0.149 0.1892 -- 100.0
X Ray Diffraction 2.2679 2.3489 -- 140 2686 0.155 0.2183 -- 100.0
X Ray Diffraction 2.3489 2.443 -- 119 2706 0.161 0.2018 -- 100.0
X Ray Diffraction 2.443 2.5541 -- 147 2677 0.162 0.1994 -- 100.0
X Ray Diffraction 2.5541 2.6888 -- 151 2684 0.1606 0.2014 -- 100.0
X Ray Diffraction 2.6888 2.8572 -- 144 2721 0.1624 0.1998 -- 100.0
X Ray Diffraction 2.8572 3.0778 -- 137 2718 0.1575 0.1888 -- 100.0
X Ray Diffraction 3.0778 3.3874 -- 151 2714 0.1504 0.1625 -- 100.0
X Ray Diffraction 3.3874 3.8774 -- 164 2711 0.1367 0.1599 -- 100.0
X Ray Diffraction 3.8774 4.8843 -- 146 2763 0.1315 0.1503 -- 100.0
X Ray Diffraction 4.8843 46.8717 -- 161 2853 0.1673 0.1674 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic and tls
Anisotropic B[1][1] 6.8621
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.8621
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.9249
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.075
f_bond_d 0.006
f_dihedral_angle_d 16.431
f_plane_restr 0.005
f_angle_d 1.188
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4286
Nucleic Acid Atoms 570
Heterogen Atoms 131
Solvent Atoms 380

Software

Software
Software Name Purpose
XDS data scaling
PHENIX model building version: (phenix.refine: dev_1009)
PHENIX refinement version: (phenix.refine: dev_1009)
XDS data reduction
PHENIX phasing version: dev_1009