X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 20%(v/v) PEG400, 0.1M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.31 α = 90
b = 69.61 β = 90
c = 117.68 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 Sagitally focusing Ge(220) and a multilayer 2011-04-21
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
2.5 20 99.7 0.073 -- -- 6.84 18608 18608 0.0 -3.0 53.502
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)
2.5 2.56 100.0 0.632 -- 3.37 6.14 1358

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 2.5 19.971 -- 0.0 17273 17273 878 93.01 0.2207 0.2207 0.2193 0.2482 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 2.5 2.6563 -- 124 2324 0.3513 0.3803 -- 81.0
X Ray Diffraction 2.6563 2.8609 -- 138 2534 0.3 0.3498 -- 88.0
X Ray Diffraction 2.8609 3.1478 -- 153 2698 0.2672 0.3305 -- 93.0
X Ray Diffraction 3.1478 3.6009 -- 171 2827 0.2399 0.2614 -- 97.0
X Ray Diffraction 3.6009 4.5281 -- 158 2933 0.1853 0.2099 -- 99.0
X Ray Diffraction 4.5281 19.9717 -- 134 3079 0.179 0.1881 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.2295
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.7581
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.5286
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.793
f_plane_restr 0.003
f_chiral_restr 0.04
f_angle_d 0.569
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3029
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 91

Software

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