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Crystal Structure of Human GGPPS Bound to Selective Inhibitor CML-07-119
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, HANGING DROP 8 293.15 100 mM Tris-HCl pH 8.0, 42% 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.413 α = 90 b = 116.167 β = 99.272 c = 214.406 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 EIGER2 XE 16M Microfocus 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
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 2.64 106.03 45.6 0.167 0.18 0.067 0.996 4.3 6.9 54508 32.88
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 2.64 3.26 9.1 0.483 0.524 0.202 0.809 1.6 6.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.641 106.027 54505 2757 45.448 0.211 0.2088 0.2088 0.2473 0.248 54.025
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] 0.601 1.08 -2.576 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.702 r_dihedral_angle_6_deg 14.108 r_dihedral_angle_2_deg 10.791 r_lrange_it 5.525 r_lrange_other 5.525 r_dihedral_angle_1_deg 5.503 r_scangle_it 3.346 r_scangle_other 3.346 r_mcangle_it 2.794 r_mcangle_other 2.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.702 r_dihedral_angle_6_deg 14.108 r_dihedral_angle_2_deg 10.791 r_lrange_it 5.525 r_lrange_other 5.525 r_dihedral_angle_1_deg 5.503 r_scangle_it 3.346 r_scangle_other 3.346 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scbond_it 1.946 r_scbond_other 1.946 r_mcbond_it 1.614 r_mcbond_other 1.614 r_angle_refined_deg 1.61 r_angle_other_deg 0.522 r_symmetry_nbd_refined 0.386 r_nbd_other 0.274 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.22 r_nbtor_refined 0.197 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_other 0.152 r_metal_ion_refined 0.119 r_ncsr_local_group_30 0.091 r_ncsr_local_group_21 0.09 r_ncsr_local_group_38 0.085 r_ncsr_local_group_60 0.085 r_ncsr_local_group_45 0.084 r_ncsr_local_group_65 0.084 r_ncsr_local_group_63 0.083 r_ncsr_local_group_11 0.082 r_ncsr_local_group_56 0.082 r_ncsr_local_group_66 0.082 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_12 0.077 r_ncsr_local_group_51 0.075 r_ncsr_local_group_24 0.074 r_ncsr_local_group_22 0.073 r_ncsr_local_group_23 0.073 r_ncsr_local_group_28 0.072 r_ncsr_local_group_26 0.071 r_ncsr_local_group_29 0.07 r_ncsr_local_group_2 0.068 r_ncsr_local_group_25 0.068 r_ncsr_local_group_27 0.068 r_chiral_restr 0.067 r_ncsr_local_group_15 0.066 r_ncsr_local_group_18 0.066 r_ncsr_local_group_1 0.065 r_ncsr_local_group_7 0.065 r_ncsr_local_group_19 0.064 r_ncsr_local_group_5 0.062 r_ncsr_local_group_13 0.062 r_ncsr_local_group_16 0.062 r_ncsr_local_group_17 0.062 r_ncsr_local_group_14 0.061 r_ncsr_local_group_33 0.061 r_ncsr_local_group_47 0.061 r_ncsr_local_group_49 0.06 r_ncsr_local_group_32 0.059 r_ncsr_local_group_42 0.059 r_ncsr_local_group_43 0.059 r_ncsr_local_group_46 0.059 r_ncsr_local_group_52 0.059 r_ncsr_local_group_3 0.058 r_ncsr_local_group_35 0.058 r_ncsr_local_group_54 0.058 r_ncsr_local_group_6 0.057 r_ncsr_local_group_20 0.057 r_ncsr_local_group_34 0.057 r_ncsr_local_group_39 0.057 r_ncsr_local_group_40 0.057 r_ncsr_local_group_41 0.057 r_ncsr_local_group_62 0.057 r_ncsr_local_group_4 0.056 r_ncsr_local_group_9 0.056 r_ncsr_local_group_57 0.056 r_ncsr_local_group_53 0.055 r_ncsr_local_group_58 0.055 r_ncsr_local_group_61 0.055 r_ncsr_local_group_10 0.054 r_ncsr_local_group_31 0.054 r_ncsr_local_group_48 0.054 r_ncsr_local_group_8 0.053 r_ncsr_local_group_64 0.052 r_ncsr_local_group_50 0.051 r_ncsr_local_group_55 0.051 r_ncsr_local_group_59 0.05 r_ncsr_local_group_37 0.049 r_ncsr_local_group_36 0.046 r_ncsr_local_group_44 0.045 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28451 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 480
Software Software Software Name Purpose REFMAC refinement DIALS data reduction STARANISO data scaling PHASER phasing