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Crystal structure of human FPPS in complex with CL01131
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F7M PDB ENTRY 2F7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 17% PEG10000, 6.8% ethylene glycol, 15% glycerol, 0.085 M HEPES, microseeding (see primary citation for details), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.87 α = 90 b = 110.87 β = 90 c = 77.03 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 RAYONIX MX-300 2012-09-25 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 2.35 49.58 99.7 0.044 36.7 14.4 20634 20573 49.8
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 2.35 2.41 98 0.527 5.4 14.4 1483
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 2F7M 2.35 49.58 19406 19406 1047 99.47 0.18399 0.18399 0.18161 0.1877 0.22962 0.2354 RANDOM 71.347
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] -3.75 -3.75 7.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 19.27 r_dihedral_angle_3_deg 15.489 r_long_range_B_refined 7.035 r_long_range_B_other 7.034 r_dihedral_angle_1_deg 5.594 r_scangle_other 5.048 r_mcangle_it 3.703 r_mcangle_other 3.702 r_scbond_it 3.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 19.27 r_dihedral_angle_3_deg 15.489 r_long_range_B_refined 7.035 r_long_range_B_other 7.034 r_dihedral_angle_1_deg 5.594 r_scangle_other 5.048 r_mcangle_it 3.703 r_mcangle_other 3.702 r_scbond_it 3.406 r_scbond_other 3.405 r_mcbond_it 2.479 r_mcbond_other 2.478 r_angle_refined_deg 1.752 r_angle_other_deg 0.847 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 31
Software Software Software Name Purpose MxDC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing