X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2870.1 M MES (pH 6.0), 15% (v/v) PEG 400, 0.1M calcium acetate
Crystal Properties
Matthews coefficientSolvent content
2.7455.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.206α = 90
b = 147.329β = 103.91
c = 95.233γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

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
12501000.1040.0620.989.13.817123423
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.061000.6220.3630.713.9

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 REPLACEMENTTHROUGHOUT5MKV250162466876899.870.184380.183340.20371RANDOM26.875
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]
-0.320.480.52-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.213
r_dihedral_angle_4_deg17.242
r_dihedral_angle_3_deg12.545
r_dihedral_angle_1_deg5.771
r_long_range_B_refined4.401
r_long_range_B_other4.4
r_scangle_other3.094
r_mcangle_it2.341
r_mcangle_other2.341
r_scbond_it1.973
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.213
r_dihedral_angle_4_deg17.242
r_dihedral_angle_3_deg12.545
r_dihedral_angle_1_deg5.771
r_long_range_B_refined4.401
r_long_range_B_other4.4
r_scangle_other3.094
r_mcangle_it2.341
r_mcangle_other2.341
r_scbond_it1.973
r_scbond_other1.972
r_mcbond_it1.491
r_mcbond_other1.491
r_angle_refined_deg1.387
r_angle_other_deg1.216
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms14833
Nucleic Acid Atoms
Solvent Atoms728
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building