X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6M0J6M0J, 5M13
experimental modelPDB 5M136M0J, 5M13

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.2 M Potassium phosphate dibasic, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.8568.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.463α = 90
b = 177.463β = 90
c = 133.13γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-12-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97853SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
13501000.1740.1840.0570.9914.19.225343
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.111001.5651.6520.5090.5691.359.7

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 REPLACEMENTTHROUGHOUT6M0J, 5M13347.8124003130799.750.227510.226430.2476RANDOM90.627
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]
1.260.631.26-4.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.715
r_dihedral_angle_4_deg14.164
r_dihedral_angle_3_deg13.003
r_scangle_other12.933
r_mcangle_other12.123
r_mcangle_it12.121
r_scbond_it8.443
r_scbond_other8.442
r_dihedral_angle_1_deg8.056
r_mcbond_it7.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.715
r_dihedral_angle_4_deg14.164
r_dihedral_angle_3_deg13.003
r_scangle_other12.933
r_mcangle_other12.123
r_mcangle_it12.121
r_scbond_it8.443
r_scbond_other8.442
r_dihedral_angle_1_deg8.056
r_mcbond_it7.969
r_mcbond_other7.946
r_angle_refined_deg1.582
r_angle_other_deg1.57
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4878
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms127

Software

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