X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VNA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.42901.36 M ammonium sulfate, 100 mM CHES pH 9.4
Crystal Properties
Matthews coefficientSolvent content
2.652.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.79α = 90
b = 80.305β = 90
c = 121.663γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCD2016-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45097.528727276
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4499.936.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5VNA2.448.6725753135497.420.189160.186190.24771RANDOM58.66
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]
-0.030.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.834
r_dihedral_angle_3_deg15.965
r_dihedral_angle_4_deg15.853
r_long_range_B_other10.537
r_long_range_B_refined10.526
r_mcangle_it7.393
r_mcangle_other7.392
r_scangle_other7.39
r_dihedral_angle_1_deg7.011
r_scbond_it5.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.834
r_dihedral_angle_3_deg15.965
r_dihedral_angle_4_deg15.853
r_long_range_B_other10.537
r_long_range_B_refined10.526
r_mcangle_it7.393
r_mcangle_other7.392
r_scangle_other7.39
r_dihedral_angle_1_deg7.011
r_scbond_it5.038
r_mcbond_it4.919
r_mcbond_other4.916
r_scbond_other4.905
r_angle_refined_deg1.643
r_angle_other_deg0.95
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4273
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing