☰ Navigation Tabs
Human farnesyl diphosphate synthase complexed with MG and minodronate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YV5 PDB entry 1YV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M NH4Cl, 20% PEG 6000, 10% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.922 α = 90 b = 110.922 β = 90 c = 67.308 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 IMAGE PLATE RIGAKU RAXIS HTC OSMIC mirrors 2007-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 20.44 99.2 0.065 0.027 20.6 6.8 31186 30937 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 95.3 0.606 0.27 2.3 5.7 4240
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 (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 1YV5 1.95 20.21 30937 29320 1573 99.25 0.17078 0.16907 0.174 0.2022 0.2084 RANDOM 28.864
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] -0.92 -0.92 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_4_deg 17.959 r_dihedral_angle_3_deg 13.61 r_scangle_it 7.711 r_scbond_it 6.085 r_dihedral_angle_1_deg 5.726 r_mcangle_it 3.637 r_mcbond_it 2.74 r_angle_refined_deg 1.47 r_angle_other_deg 1.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_4_deg 17.959 r_dihedral_angle_3_deg 13.61 r_scangle_it 7.711 r_scbond_it 6.085 r_dihedral_angle_1_deg 5.726 r_mcangle_it 3.637 r_mcbond_it 2.74 r_angle_refined_deg 1.47 r_angle_other_deg 1.353 r_mcbond_other 0.827 r_nbd_refined 0.208 r_symmetry_vdw_other 0.196 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.18 r_nbd_other 0.179 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.088 r_chiral_restr 0.085 r_symmetry_vdw_refined 0.045 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing