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 = 108.86 α = 90
b = 108.86 β = 90
c = 91 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
CCD MARMOSAIC 225 mm CCD -- 2010-05-20
Diffraction Radiation
Monochromator Protocol
Bartels Monochromator with dual channel cut crystals (DCCM) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA

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
2.19 50 98.5 -- -- -- -- 32014 32014 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)
2.19 2.32 90.6 0.802 -- 2.06 -- --

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 2.2 47.138 -- 2.0 31776 31776 1598 99.22 -- 0.1627 0.1602 0.2088 --
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 2.2 2.271 -- 119 2538 0.2399 0.2984 -- 92.0
X Ray Diffraction 2.271 2.3522 -- 139 2723 0.2029 0.2727 -- 100.0
X Ray Diffraction 2.3522 2.4464 -- 123 2750 0.1965 0.2712 -- 100.0
X Ray Diffraction 2.4464 2.5577 -- 151 2721 0.19 0.2725 -- 100.0
X Ray Diffraction 2.5577 2.6925 -- 148 2740 0.1656 0.2589 -- 100.0
X Ray Diffraction 2.6925 2.8612 -- 151 2748 0.167 0.2223 -- 100.0
X Ray Diffraction 2.8612 3.0821 -- 142 2757 0.1566 0.222 -- 100.0
X Ray Diffraction 3.0821 3.3922 -- 148 2761 0.1539 0.2033 -- 100.0
X Ray Diffraction 3.3922 3.8828 -- 162 2745 0.1452 0.186 -- 100.0
X Ray Diffraction 3.8828 4.8911 -- 152 2802 0.1347 0.1736 -- 100.0
X Ray Diffraction 4.8911 47.1486 -- 163 2893 0.1609 0.1893 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic and tls
Anisotropic B[1][1] 7.6072
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.6072
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.8507
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.07
f_dihedral_angle_d 16.647
f_angle_d 1.129
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4286
Nucleic Acid Atoms 569
Heterogen Atoms 111
Solvent Atoms 245

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.2_869) Structure Solution
PHENIX (phenix.refine: dev_1009) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
PHENIX version: (phenix.refine: 1.7.2_869) model building
XDS data collection