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PcIDS1_F315D in complex with Mg2+ and GPP
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 8.5 293 0.1 M TRIS, 0.5 M LiCl, 28% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 78.12 β = 101.44 c = 88.13 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 2020-02-16 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 1.55 30 94.9 0.039 13.1 2.8 107827
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 1.55 1.65 98.2 0.509 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8A6U 1.55 15 102435 5392 94.96 0.1481 0.146 0.1456 0.1865 0.1872 RANDOM 26.745
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] 1.09 0.59 -0.45 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.386 r_dihedral_angle_4_deg 16.8 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_1_deg 5.43 r_rigid_bond_restr 3.46 r_angle_refined_deg 1.785 r_angle_other_deg 1.56 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.386 r_dihedral_angle_4_deg 16.8 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_1_deg 5.43 r_rigid_bond_restr 3.46 r_angle_refined_deg 1.785 r_angle_other_deg 1.56 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5314 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing