X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VAWPDB entry 3vaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290Internal tracking number 224744. JCSG well D10. 0.1M Cacodylate pH 6.5, 200mM Calcium Acetate, 30.0% w/v PEG400, 20% Ethylene Glycol Cryo. BupsA.00130.a.D239 PD00214 21.8mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
3.0960.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.44α = 90
b = 49.05β = 123.05
c = 66.64γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1244.6197.50.04726.886.441974419250-3-323.506
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0596.60.1319.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTPDB entry 3vaw244.61197441875595095.290.220.220.2190.247RANDOM21.826
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.94-0.351.09-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.937
r_dihedral_angle_4_deg21.543
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg6.664
r_angle_refined_deg1.473
r_angle_other_deg0.89
r_chiral_restr0.071
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.937
r_dihedral_angle_4_deg21.543
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg6.664
r_angle_refined_deg1.473
r_angle_other_deg0.89
r_chiral_restr0.071
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1650
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms116

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction