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Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate and isopentenyl pyrophosphate
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.0 M NaCl, 0.08 M sodium acetate, 0.02 M acetic acid
Crystal Properties Matthews coefficient Solvent content 2.75 55.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.627 α = 90 b = 111.627 β = 90 c = 72.553 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 293 CCD ADSC QUANTUM 210r 2014-06-14 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE CUSTOM-MADE 2014-03-06 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A 2 NUCLEAR REACTOR 3.2-6.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.7 44.31 97.7 0.097 8.6 49965 2 2.4 22.16 98.1 0.198 2.8 18171
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.73 0.777 6.4 2.4 2.49 0.379 2.7
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT 1.7 35.3 49901 49901 2499 96.85 0.1974 0.1966 0.2011 0.2113 0.2101 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.4 22.119 18151 18151 904 98.44 0.2613 0.2599 0.2866
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.852 f_angle_d 1.082 f_chiral_restr 0.183 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement STARGazer data reduction HKL-2000 data scaling MOLREP phasing