X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IVV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82950.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Crystal Properties
Matthews coefficientSolvent content
2.0339.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.4α = 89.25
b = 55.17β = 89.89
c = 58.07γ = 86.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2M2015-07-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.0310096.40.1068.623.5412407632906
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.102

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 REPLACEMENTTHROUGHOUT3IVV2.0319.8532906165097.970.188060.184140.26169RANDOM38.798
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]
-0.010.01-0.010.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.658
r_dihedral_angle_4_deg16.619
r_dihedral_angle_3_deg15.881
r_long_range_B_refined7.893
r_long_range_B_other7.849
r_dihedral_angle_1_deg7.717
r_scangle_other5.284
r_mcangle_it4.715
r_mcangle_other4.714
r_scbond_it3.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.658
r_dihedral_angle_4_deg16.619
r_dihedral_angle_3_deg15.881
r_long_range_B_refined7.893
r_long_range_B_other7.849
r_dihedral_angle_1_deg7.717
r_scangle_other5.284
r_mcangle_it4.715
r_mcangle_other4.714
r_scbond_it3.421
r_scbond_other3.42
r_mcbond_other3.167
r_mcbond_it3.166
r_angle_refined_deg1.693
r_angle_other_deg1.003
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms4760
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing