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Crystal structure of human FPPS in complex with [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H5C PDB ENTRY 4H5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 1.7M sodium chloride, 15% glycerol, 0.085M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.06 α = 90 b = 111.06 β = 90 c = 67.03 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 RIGAKU SATURN 944+ Rigaku Varimax-HF 2014-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 111.06 98.8 0.067 44.1 32.9 26578 26578 22.614
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 90.9 0.397 2.5 3 1769
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4H5C 2.05 111.06 25246 25246 1288 98.7 0.1622 0.1622 0.15999 0.1716 0.20573 0.2167 RANDOM 32.252
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] -1.98 -1.98 3.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 21.795 r_dihedral_angle_3_deg 13.885 r_long_range_B_refined 6.581 r_long_range_B_other 6.58 r_dihedral_angle_1_deg 5.62 r_scangle_other 3.029 r_mcangle_it 2.013 r_mcangle_other 2.013 r_scbond_it 1.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 21.795 r_dihedral_angle_3_deg 13.885 r_long_range_B_refined 6.581 r_long_range_B_other 6.58 r_dihedral_angle_1_deg 5.62 r_scangle_other 3.029 r_mcangle_it 2.013 r_mcangle_other 2.013 r_scbond_it 1.943 r_scbond_other 1.943 r_angle_refined_deg 1.786 r_mcbond_it 1.316 r_mcbond_other 1.314 r_angle_other_deg 0.919 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2769 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 35
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing