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Crystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-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 5.6% PEG 4000, 30% glycerol, 0.07M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.26 α = 90 b = 111.26 β = 90 c = 69.34 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 2014-01-07 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 2.18 69.34 98.6 0.062 53.8 19.7 22981 22981 28.4
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 2.18 2.24 98.9 0.653 3.5 10.9 1671
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 2.18 69.34 21774 21774 1167 98.58 0.17229 0.17229 0.16974 0.182 0.22008 0.2347 RANDOM 38.974
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] -2.82 -2.82 5.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.289 r_dihedral_angle_4_deg 18.67 r_dihedral_angle_3_deg 15.101 r_dihedral_angle_1_deg 5.621 r_long_range_B_refined 5.438 r_long_range_B_other 5.438 r_scangle_other 3.515 r_mcangle_it 2.321 r_mcangle_other 2.32 r_scbond_it 2.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.289 r_dihedral_angle_4_deg 18.67 r_dihedral_angle_3_deg 15.101 r_dihedral_angle_1_deg 5.621 r_long_range_B_refined 5.438 r_long_range_B_other 5.438 r_scangle_other 3.515 r_mcangle_it 2.321 r_mcangle_other 2.32 r_scbond_it 2.287 r_scbond_other 2.286 r_angle_refined_deg 1.707 r_mcbond_it 1.612 r_mcbond_other 1.61 r_angle_other_deg 0.909 r_chiral_restr 0.095 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2751 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 35
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing