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Crystal structure (II) of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL03049
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295.15 0.085 M tri-Sodium citrate (pH 5.6), 0.425 M Ammonium sulfate, 0.85 M Lithium sulfate, 15% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.45 α = 90 b = 110.45 β = 90 c = 77 γ = 90
Symmetry Space Group P 41 21 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 RAYONIX MX-300 2016-04-21 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) 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 2.65 63.17 99 0.049 0.054 0.017 28 9.7 14144 64.957
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.72 98.7 1.082 1.181 0.366 3 9.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.652 63.165 14109 708 98.506 0.164 0.1616 0.1738 0.2183 0.2251 Random 90.169
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] -6.555 -6.555 13.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.278 r_dihedral_angle_6_deg 14.146 r_lrange_it 11.36 r_lrange_other 11.359 r_dihedral_angle_2_deg 8.061 r_scangle_it 7.8 r_scangle_other 7.79 r_dihedral_angle_1_deg 6.343 r_mcangle_it 5.385 r_mcangle_other 5.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.278 r_dihedral_angle_6_deg 14.146 r_lrange_it 11.36 r_lrange_other 11.359 r_dihedral_angle_2_deg 8.061 r_scangle_it 7.8 r_scangle_other 7.79 r_dihedral_angle_1_deg 6.343 r_mcangle_it 5.385 r_mcangle_other 5.383 r_scbond_it 5.284 r_scbond_other 5.273 r_mcbond_it 3.544 r_mcbond_other 3.544 r_chiral_restr_other 3.32 r_angle_refined_deg 1.662 r_angle_other_deg 0.648 r_nbd_refined 0.237 r_nbtor_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_other 0.182 r_symmetry_nbd_refined 0.175 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.157 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2685 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing