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X-ray structure of Farnesyl diphosphate synthase protein
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 4 293 14% PEG 6000, 0.7 M LiCl, 70 mM citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.255 α = 90 b = 112.255 β = 90 c = 63.245 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 MARRESEARCH 2005-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.984 SLS X10SA
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 2.3 63 95.6 0.1 0.11 13.9 5.2 18323 17517 38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 97.9 2.7 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1YV5 2.3 30 17553 16605 886 94.59 0.17508 0.17508 0.17249 0.22311 0.2523 RANDOM 46.785
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] -3.86 -3.86 7.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.947 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 15.64 r_scangle_it 7.394 r_scbond_it 5.873 r_dihedral_angle_1_deg 5.53 r_mcangle_it 3.529 r_mcbond_it 2.427 r_angle_refined_deg 1.504 r_angle_other_deg 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.947 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 15.64 r_scangle_it 7.394 r_scbond_it 5.873 r_dihedral_angle_1_deg 5.53 r_mcangle_it 3.529 r_mcbond_it 2.427 r_angle_refined_deg 1.504 r_angle_other_deg 0.84 r_mcbond_other 0.648 r_symmetry_vdw_other 0.239 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.203 r_nbtor_refined 0.185 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.139 r_symmetry_vdw_refined 0.13 r_nbtor_other 0.087 r_chiral_restr 0.079 r_metal_ion_refined 0.047 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 2697 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling