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PcIDS1 in complex with Mg2+ and IPP
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, 0.2 M MgCl2, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.4 α = 90 b = 72.4 β = 101.53 c = 84.9 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 2018-12-01 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 1.9 30 98.3 0.053 11.8 3.1 52944
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 1.9 2 0.593 2
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 8A6U 1.9 15 50190 2642 98.16 0.1659 0.164 0.1744 0.2029 0.2127 RANDOM 33.264
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] -1.27 -2.35 0.02 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 15.586 r_dihedral_angle_3_deg 14.007 r_dihedral_angle_1_deg 5.25 r_angle_refined_deg 1.167 r_angle_other_deg 1.135 r_rigid_bond_restr 0.396 r_chiral_restr 0.054 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 15.586 r_dihedral_angle_3_deg 14.007 r_dihedral_angle_1_deg 5.25 r_angle_refined_deg 1.167 r_angle_other_deg 1.135 r_rigid_bond_restr 0.396 r_chiral_restr 0.054 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5458 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing