X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.75
Temperature 293.0
Details 100mM HEPES, 200mM MgCl2, 25% PEG4000, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.8 α = 90
b = 83.8 β = 90
c = 142.57 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Si(111) 2008-06-26
Diffraction Radiation
Monochromator Protocol
DCM Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45 LNLS W01B-MX2

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
2.63 50.1 97.3 -- -- -- -- 9392 9139 2.0 2.0 --
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)
2.63 -- 97.3 -- -- -- -- --

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 2.63 50.855 -- 1.36 9392 9125 436 97.6 -- 0.2391 0.2386 0.2503 --
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 2.63 3.0106 -- 164 2767 0.319 0.3167 -- 97.0
X Ray Diffraction 3.0106 3.7928 -- 139 2880 0.2264 0.2544 -- 99.0
X Ray Diffraction 3.7928 50.8648 -- 133 3042 0.227 0.2282 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.7314
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.7314
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.4629
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.073
f_dihedral_angle_d 18.203
f_angle_d 1.115
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1218
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 21

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 2011_09_22_2056) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser molecular replacement