X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K8V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.150.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
3.3262.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.892α = 90
b = 61.054β = 94.57
c = 105.704γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.9793NSLS-II17-ID-2

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
11.7128.7697.80.0390.0550.0390.99810.51.958990
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)
11.711.7494.50.4370.6180.4370.731.9

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 REPLACEMENTTHROUGHOUTPDB entry 4K8V1.7128.7656000298997.770.178990.177220.21139RANDOM27.339
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]
-1.170.37-1.292.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.038
r_long_range_B_refined9.754
r_long_range_B_other9.733
r_dihedral_angle_2_deg7.625
r_scangle_other7.253
r_dihedral_angle_1_deg6.198
r_mcangle_it4.726
r_mcangle_other4.726
r_scbond_it4.632
r_scbond_other4.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.038
r_long_range_B_refined9.754
r_long_range_B_other9.733
r_dihedral_angle_2_deg7.625
r_scangle_other7.253
r_dihedral_angle_1_deg6.198
r_mcangle_it4.726
r_mcangle_other4.726
r_scbond_it4.632
r_scbond_other4.631
r_mcbond_it3.337
r_mcbond_other3.335
r_angle_refined_deg1.642
r_angle_other_deg0.539
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms2954
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms1

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement