X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.4
Temperature 291.0
Details 50 mM Tris HCl pH=8.4, 0.2 M NH4Cl, 10 mM CaCl2, 34% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.21 α = 90
b = 109.21 β = 90
c = 91.05 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 PSI PILATUS 6M Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator 2010-08-13
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
1.89 50 99.3 0.118 -- -- -- 50305 50305 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)
1.89 2.0 95.6 1.182 -- 1.2 -- --

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 1.9 47.291 -- 2.0 49722 49722 2491 99.97 -- 0.1785 0.1765 0.2157 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 1.9 1.9366 -- 131 2582 0.2918 0.3147 -- 100.0
X Ray Diffraction 1.9366 1.9761 -- 141 2598 0.2523 0.2869 -- 100.0
X Ray Diffraction 1.9761 2.0191 -- 152 2622 0.2421 0.3034 -- 100.0
X Ray Diffraction 2.0191 2.066 -- 126 2568 0.2303 0.2411 -- 100.0
X Ray Diffraction 2.066 2.1177 -- 143 2607 0.2123 0.2428 -- 100.0
X Ray Diffraction 2.1177 2.1749 -- 122 2591 0.2056 0.23 -- 100.0
X Ray Diffraction 2.1749 2.2389 -- 120 2607 0.2042 0.2475 -- 100.0
X Ray Diffraction 2.2389 2.3112 -- 142 2616 0.1986 0.2593 -- 100.0
X Ray Diffraction 2.3112 2.3938 -- 118 2625 0.1782 0.238 -- 100.0
X Ray Diffraction 2.3938 2.4897 -- 129 2627 0.1735 0.2256 -- 100.0
X Ray Diffraction 2.4897 2.603 -- 146 2611 0.1703 0.219 -- 100.0
X Ray Diffraction 2.603 2.7402 -- 148 2604 0.1736 0.2299 -- 100.0
X Ray Diffraction 2.7402 2.9118 -- 138 2625 0.1869 0.2226 -- 100.0
X Ray Diffraction 2.9118 3.1366 -- 132 2640 0.1786 0.2613 -- 100.0
X Ray Diffraction 3.1366 3.4522 -- 150 2615 0.1624 0.1881 -- 100.0
X Ray Diffraction 3.4522 3.9515 -- 155 2644 0.1426 0.1787 -- 100.0
X Ray Diffraction 3.9515 4.9776 -- 141 2671 0.1391 0.1811 -- 100.0
X Ray Diffraction 4.9776 47.3052 -- 157 2778 0.1739 0.1915 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic and tls
Anisotropic B[1][1] 5.1587
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.1587
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.1226
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.172
f_chiral_restr 0.071
f_bond_d 0.007
f_plane_restr 0.005
f_dihedral_angle_d 16.929
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4286
Nucleic Acid Atoms 520
Heterogen Atoms 77
Solvent Atoms 323

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