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Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 0.085 M HEPES (pH 7.5), 17% (w/v) PEG 10000, 6.8% (v/v) ethylene glycol, 15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.95 α = 90 b = 110.95 β = 90 c = 73.9 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 2014-09-19 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 2.2 49.62 98.9 0.041 0.045 0.015 24.7 8.9 23662 59.516
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 2.2 2.26 97.2 1.004 1.126 0.374 2.2 8.6
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 2.2 49.618 23638 1197 98.541 0.191 0.1882 0.2116 0.2462 0.2648 Random 81.006
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] -5.027 -5.027 10.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.044 r_dihedral_angle_3_deg 14.331 r_dihedral_angle_2_deg 11.39 r_lrange_other 9.385 r_lrange_it 9.381 r_scangle_it 6.592 r_scangle_other 6.59 r_dihedral_angle_1_deg 6.031 r_mcangle_it 4.771 r_mcangle_other 4.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.044 r_dihedral_angle_3_deg 14.331 r_dihedral_angle_2_deg 11.39 r_lrange_other 9.385 r_lrange_it 9.381 r_scangle_it 6.592 r_scangle_other 6.59 r_dihedral_angle_1_deg 6.031 r_mcangle_it 4.771 r_mcangle_other 4.77 r_scbond_other 4.394 r_scbond_it 4.393 r_mcbond_it 3.298 r_mcbond_other 3.295 r_angle_refined_deg 1.435 r_angle_other_deg 0.502 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.193 r_symmetry_nbd_other 0.189 r_nbd_other 0.151 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_refined 0.062 r_symmetry_nbd_refined 0.035 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing