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Structure of mutant human geranylgeranyl pyrophosphate synthase (Y246D-C247L) in complex with isopentenyl pyrophosphate
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 295.15 0.2 M di-ammonium phosphate, 2.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.4 63.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.11 α = 90 b = 191.11 β = 90 c = 96.63 γ = 120
Symmetry Space Group P 6 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 PIXEL DECTRIS PILATUS3 S 6M 2019-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 95.56 99.9 0.101 0.104 0.023 1 20.4 19.6 60724 40.173
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.1 1.683 1.736 0.419 0.665 1.6 16.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.1 95.555 60724 3000 99.849 0.18 0.1803 0.1785 0.1872 0.2159 0.2213 Random 46.684
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] 0.514 0.257 0.514 -1.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.629 r_dihedral_angle_3_deg 14.305 r_lrange_it 10.468 r_lrange_other 10.378 r_scangle_it 8.98 r_scangle_other 8.828 r_dihedral_angle_2_deg 6.96 r_scbond_it 6.324 r_scbond_other 6.053 r_mcangle_it 5.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.629 r_dihedral_angle_3_deg 14.305 r_lrange_it 10.468 r_lrange_other 10.378 r_scangle_it 8.98 r_scangle_other 8.828 r_dihedral_angle_2_deg 6.96 r_scbond_it 6.324 r_scbond_other 6.053 r_mcangle_it 5.972 r_mcangle_other 5.971 r_dihedral_angle_1_deg 5.285 r_mcbond_it 4.62 r_mcbond_other 4.619 r_angle_refined_deg 1.725 r_angle_other_deg 0.615 r_dihedral_angle_other_2_deg 0.433 r_symmetry_xyhbond_nbd_refined 0.382 r_nbd_refined 0.236 r_symmetry_nbd_refined 0.222 r_xyhbond_nbd_refined 0.207 r_nbtor_refined 0.193 r_symmetry_nbd_other 0.185 r_nbd_other 0.185 r_ncsr_local_group_1 0.141 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4599 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing