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PcIDS1 in complex with Mg2+/Mn2+, IPP, and ZOL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8A6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M BIS-TRIS, 0.1 M MgCl2, 26% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.08 α = 90 b = 70.48 β = 91.29 c = 94.9 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 EIGER X 16M 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.3 30 96 0.043 12.1 3.1 180288
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.4 94.4 0.552 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8A6U 1.3 15 171154 9008 95.97 0.1435 0.1422 0.1681 0.1868 RANDOM 19.276
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] -1.11 -0.17 -1 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.751 r_dihedral_angle_4_deg 17.941 r_dihedral_angle_3_deg 13.13 r_dihedral_angle_1_deg 5.337 r_rigid_bond_restr 4.779 r_angle_refined_deg 2.066 r_angle_other_deg 1.708 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.751 r_dihedral_angle_4_deg 17.941 r_dihedral_angle_3_deg 13.13 r_dihedral_angle_1_deg 5.337 r_rigid_bond_restr 4.779 r_angle_refined_deg 2.066 r_angle_other_deg 1.708 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5608 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing