X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.3
Temperature 293.0
Details 40% (v/v) MPD, 0.2 M CaCl2, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.14 α = 90
b = 39.14 β = 90
c = 118.19 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-08-15
CCD MARMOSAIC 225 mm CCD -- 2009-07-10
Diffraction Radiation
Monochromator Protocol
Bartels Monochromator (Si 111) SINGLE WAVELENGTH
Silicon 111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.0722 SLS X06DA
SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2

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
1.5 20 98.6 -- 0.05 -- 12.5 16414 16181 -- -3.0 22.7
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)
1.5 1.54 97.4 -- 0.27 8.95 12.09 --

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
SAD, MOLECULAR REPLACEMENT 1.5 19.389 -- 2.04 16414 16144 806 98.65 -- 0.1601 0.1589 0.1817 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 1.5001 1.594 -- 131 2504 0.1567 0.1673 -- 98.0
X Ray Diffraction 1.594 1.717 -- 135 2559 0.151 0.1746 -- 99.0
X Ray Diffraction 1.717 1.8897 -- 135 2575 0.1618 0.1838 -- 99.0
X Ray Diffraction 1.8897 2.1628 -- 135 2568 0.1424 0.1941 -- 99.0
X Ray Diffraction 2.1628 2.7237 -- 136 2582 0.1461 0.1694 -- 99.0
X Ray Diffraction 2.7237 19.3906 -- 134 2550 0.1663 0.1805 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.4388
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.4388
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.8777
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 15.787
f_angle_d 1.245
f_bond_d 0.013
f_chiral_restr 0.074
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 536
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 107

Software

Software
Software Name Purpose
MAR345dtb data collection
SHELX model building version: (anomalous dataset)
ARP/wARP model building
PHENIX refinement version: (phenix.refine: 1.6_289)
XDS data reduction
XSCALE data scaling
SHELX phasing version: (anomalous dataset)