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Crystal structure of human FPPS in complex with nickel, JDS05120, and sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H5D PDB ENTRY 4H5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 0.85M lithium sulfate, 0.01M nickel chloride, 15% glycerol, 0.09M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.94 α = 90 b = 110.94 β = 90 c = 68.46 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 2013-05-05 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) 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 1.85 51.58 98.7 0.049 25.8 9.8 36445 36445 23.7
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 1.85 1.9 97.7 0.47 4.7 9.6 2615
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 4H5D 1.85 51.58 34008 34008 1795 97.14 0.1534 0.1534 0.15184 0.1659 0.18195 0.1937 RANDOM 39.154
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] -2.95 -2.95 5.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.203 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 13.808 r_long_range_B_refined 6.629 r_long_range_B_other 6.628 r_dihedral_angle_1_deg 5.288 r_scangle_other 4.6 r_scbond_other 3.109 r_scbond_it 3.105 r_mcangle_it 2.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.203 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 13.808 r_long_range_B_refined 6.629 r_long_range_B_other 6.628 r_dihedral_angle_1_deg 5.288 r_scangle_other 4.6 r_scbond_other 3.109 r_scbond_it 3.105 r_mcangle_it 2.426 r_mcangle_other 2.426 r_angle_refined_deg 1.837 r_mcbond_it 1.836 r_mcbond_other 1.826 r_angle_other_deg 0.939 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2745 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 34
Software Software Software Name Purpose MxDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing