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Crystal Structure (I) 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 4.6 295.15 0.08 M Sodium acetate (pH 4.6), 0.16 M Ammonium sulfate, 20% (w/v) PEG 4000, 20% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.04 α = 90 b = 111.04 β = 90 c = 73.98 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 2014-09-14 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 2.4 49.66 99.4 0.051 0.058 0.021 17.5 7.2 18514 63.164
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 2.4 2.46 99.1 0.948 1.103 0.402 1.8 7.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.4 49.659 18491 920 99.227 0.186 0.1828 0.2416 0.2399 87.403
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] -6.028 -6.028 12.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.927 r_dihedral_angle_6_deg 14.697 r_lrange_it 11.335 r_lrange_other 11.335 r_scangle_it 8.897 r_scangle_other 8.895 r_mcangle_other 6.359 r_mcangle_it 6.355 r_dihedral_angle_1_deg 6.3 r_scbond_it 5.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.927 r_dihedral_angle_6_deg 14.697 r_lrange_it 11.335 r_lrange_other 11.335 r_scangle_it 8.897 r_scangle_other 8.895 r_mcangle_other 6.359 r_mcangle_it 6.355 r_dihedral_angle_1_deg 6.3 r_scbond_it 5.982 r_scbond_other 5.98 r_dihedral_angle_2_deg 5.765 r_mcbond_it 4.239 r_mcbond_other 4.239 r_chiral_restr_other 3.281 r_angle_refined_deg 1.629 r_angle_other_deg 0.618 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.195 r_symmetry_nbd_other 0.192 r_nbd_other 0.154 r_symmetry_nbd_refined 0.102 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2676 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing