☰ Navigation Tabs
Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.5M NaCl, 0.1M acetate buffer
Crystal Properties Matthews coefficient Solvent content 2.78 55.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.966 α = 90 b = 111.966 β = 90 c = 72.754 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 270 2013-11-17 M SINGLE WAVELENGTH 2 1 neutron 293 OSCILLATION CAMERA CUSTOM-MADE 2013-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 3.99 JPARC MLF BL-03
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 1.4 50.07 96.2 0.062 7.1 87200 2 2.4 53.57 96.2 0.107 3.8 18415
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 1.4 1.42 0.482 3.2 2 2.4 2.49 0.612 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 1.402 50.07 87160 87160 4389 96.22 0.1948 0.1936 0.1888 0.2183 0.2263 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.4 53.57 18386 18386 902 98.47 0.1878 0.1857 0.2292
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 18.782 f_angle_d 0.919 f_chiral_restr 0.139 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing HKL-2000 data collection