X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D8D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52930.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
2VAPOR DIFFUSION, SITTING DROP4.52930.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
3VAPOR DIFFUSION, SITTING DROP4.52930.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3246.97
2.3246.97
2.3246.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.11α = 90
b = 122.11β = 90
c = 145.89γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9Mfocusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration2020-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98011SOLEILPROXIMA 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
13.3248.6894.60.2180.2190.018133.6155.49209
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)
13.3243.4642.19.1369.1630.710.4861.1165.4

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 REPLACEMENTTHROUGHOUT4d8d3.3248.68828392392.240.287630.286160.29953RANDOM150.582
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]
0.980.490.98-3.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.738
r_dihedral_angle_3_deg19.364
r_dihedral_angle_4_deg16.445
r_dihedral_angle_1_deg6.355
r_angle_refined_deg1.203
r_angle_other_deg1.003
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.738
r_dihedral_angle_3_deg19.364
r_dihedral_angle_4_deg16.445
r_dihedral_angle_1_deg6.355
r_angle_refined_deg1.203
r_angle_other_deg1.003
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2737
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
MOLREPphasing