X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.15
Details 0.16M Calcium Acetate, 0.08M Sodium Cacodylate, 8% PEG8000, 5% Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.88 α = 90
b = 71.09 β = 115.53
c = 88.85 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M cylindrical grazing incidence mirror 2011-08-29
Diffraction Radiation
Monochromator Protocol
liquid nitrogen cooled channel-cut silicon (Si) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97932 ESRF ID29

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
2.4 80.2 97.0 0.095 0.095 -- 2.7 39190 38014 0.0 -1.0 45.4
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)
2.4 2.53 97.7 0.645 0.645 1.1 2.6 5564

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 2.4 53.192 -- 0.0 39346 36151 1815 91.88 -- 0.1816 0.1787 0.2348 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 2.4001 2.465 2365 119 2365 0.2341 0.2757 -- 82.0
X Ray Diffraction 2.465 2.5375 2539 122 2539 0.2388 0.3421 -- 89.0
X Ray Diffraction 2.5375 2.6194 2534 142 2534 0.2408 0.3281 -- 89.0
X Ray Diffraction 2.6194 2.713 2572 135 2572 0.2205 0.2984 -- 90.0
X Ray Diffraction 2.713 2.8217 2596 128 2596 0.212 0.2545 -- 91.0
X Ray Diffraction 2.8217 2.9501 2635 135 2635 0.2067 0.2922 -- 92.0
X Ray Diffraction 2.9501 3.1056 2600 173 2600 0.1931 0.2641 -- 92.0
X Ray Diffraction 3.1056 3.3001 2755 148 2755 0.1727 0.2506 -- 96.0
X Ray Diffraction 3.3001 3.5549 2780 125 2780 0.169 0.2252 -- 95.0
X Ray Diffraction 3.5549 3.9125 2684 133 2684 0.1627 0.2207 -- 94.0
X Ray Diffraction 3.9125 4.4784 2768 166 2768 0.1439 0.198 -- 96.0
X Ray Diffraction 4.4784 5.6414 2745 147 2745 0.1521 0.1981 -- 95.0
X Ray Diffraction 5.6414 53.2052 2763 142 2763 0.1826 0.2087 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.6077
Anisotropic B[1][1] 10.1832
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -7.3665
Anisotropic B[2][2] -7.0556
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.1276
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.072
f_dihedral_angle_d 20.255
f_angle_d 1.02
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4822
Nucleic Acid Atoms 738
Heterogen Atoms 2
Solvent Atoms 255

Software

Computing
Computing Package Purpose
MxCuBe Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
MxCuBe data collection