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_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 16.431
f_angle_d 1.188
f_bond_d 0.006
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

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1009) Structure Solution
PHENIX (phenix.refine: dev_1009) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1009) refinement
PHENIX version: (phenix.refine: dev_1009) model building
XDS data collection