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Crystal structure of VinK-VinL covalent complex formed with a pantetheineamide cross-linking probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG8000, magnesium chloride, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.282 α = 90 b = 148.224 β = 91.08 c = 68.791 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2021-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 50 99 0.047 0.065 0.998 9.3 3.3 63757
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.9 0.332 0.462 0.896 2 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CZD 1.95 40.16 60569 3149 98.96 0.1957 0.1933 0.2039 0.2414 0.2519 RANDOM 33.219
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] -0.68 1.66 -0.38 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.911 r_dihedral_angle_4_deg 13.124 r_dihedral_angle_3_deg 12.278 r_dihedral_angle_1_deg 6.756 r_angle_refined_deg 1.849 r_angle_other_deg 1.617 r_chiral_restr 0.156 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.911 r_dihedral_angle_4_deg 13.124 r_dihedral_angle_3_deg 12.278 r_dihedral_angle_1_deg 6.756 r_angle_refined_deg 1.849 r_angle_other_deg 1.617 r_chiral_restr 0.156 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6004 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing Coot model building