X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VTZPDB ENTRY 3VTZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289JCSG(d2): 30% PEG 400, 200mM MgCl2, 0.1M HEPES/NaOH pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1542.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.44α = 90
b = 130.39β = 90
c = 114.12γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium Lenses2013-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97857APS21-ID-F

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
11.75099.70.07319.045.85157651407-321.808
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)
11.71.7496.90.473.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3VTZ1.7505401851407261199.670.15210.15210.15060.1807RANDOM16.709
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]
-0.290.34-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.648
r_dihedral_angle_4_deg20.745
r_dihedral_angle_3_deg12.679
r_dihedral_angle_1_deg6.473
r_angle_refined_deg1.5
r_mcangle_it1.275
r_angle_other_deg0.833
r_mcbond_other0.762
r_mcbond_it0.761
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.648
r_dihedral_angle_4_deg20.745
r_dihedral_angle_3_deg12.679
r_dihedral_angle_1_deg6.473
r_angle_refined_deg1.5
r_mcangle_it1.275
r_angle_other_deg0.833
r_mcbond_other0.762
r_mcbond_it0.761
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3287
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction