X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE298PEG 6000 30%
Crystal Properties
Matthews coefficientSolvent content
3.4163.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.633α = 90
b = 77.633β = 90
c = 77.633γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2017-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.58501000.0430.4210.64667.37.710867
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.610.4210.646

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 REPLACEMENTTHROUGHOUT5VIZ1.5831.719698109799.350.183460.181540.20112RANDOM23.648
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.986
r_dihedral_angle_3_deg12.117
r_dihedral_angle_1_deg7.419
r_long_range_B_refined6.696
r_long_range_B_other6.679
r_scangle_other5.117
r_mcangle_other4.537
r_mcangle_it4.399
r_dihedral_angle_4_deg3.716
r_scbond_it3.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.986
r_dihedral_angle_3_deg12.117
r_dihedral_angle_1_deg7.419
r_long_range_B_refined6.696
r_long_range_B_other6.679
r_scangle_other5.117
r_mcangle_other4.537
r_mcangle_it4.399
r_dihedral_angle_4_deg3.716
r_scbond_it3.377
r_scbond_other3.29
r_mcbond_it2.839
r_mcbond_other2.347
r_angle_refined_deg1.983
r_angle_other_deg1.651
r_chiral_restr0.115
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.001
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 Atoms398
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CrystalClearphasing