☰ Navigation Tabs
Crystal structure of mutant human geranylgeranyl pyrophosphate synthase (Y246D) in complex with bisphosphonate inhibitor FV0109
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 1.7 M ammonium sulfate, 4.25% isopropanol, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 3.28 62.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.45 α = 90 b = 185.45 β = 90 c = 114.2 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2017-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.38052 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.5 97.24 100 0.051 0.015 26.9 12.9 12861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.59 99.9 1.271 0.385 2.1 12.5
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 2Q80 3.5 97.24 12192 669 99.94 0.20085 0.19802 0.1991 0.25221 0.2511 RANDOM 160.71
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] -2.1 -2.1 4.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_3_deg 19.631 r_dihedral_angle_4_deg 16.735 r_long_range_B_refined 13.965 r_long_range_B_other 13.964 r_scangle_other 11.185 r_mcangle_it 9.907 r_mcangle_other 9.905 r_dihedral_angle_1_deg 7.632 r_scbond_it 7.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_3_deg 19.631 r_dihedral_angle_4_deg 16.735 r_long_range_B_refined 13.965 r_long_range_B_other 13.964 r_scangle_other 11.185 r_mcangle_it 9.907 r_mcangle_other 9.905 r_dihedral_angle_1_deg 7.632 r_scbond_it 7.486 r_scbond_other 7.484 r_mcbond_it 6.743 r_mcbond_other 6.743 r_angle_refined_deg 2.001 r_angle_other_deg 1.152 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4108 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing