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Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP and calcium bound in active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LVS PDB ENTRY 3LVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.2 M calcium acetate, 0.1 M MES/NaOH, pH 6, 20% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.899 α = 90 b = 83.117 β = 108.95 c = 71.332 γ = 90
Symmetry Space Group P 1 21 1
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 MX225HE 2013-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.55 50 96.1 0.075 16.2 3.8 81341 78181
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 1.55 1.58 93.7 0.684 2.1 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3LVS 1.55 26.46 74260 3896 96.05 0.17564 0.17418 0.20379 0.2125 RANDOM 20.307
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] -0.23 0.31 -0.22 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.573 r_dihedral_angle_4_deg 18.102 r_dihedral_angle_3_deg 13.777 r_long_range_B_refined 5.871 r_long_range_B_other 5.844 r_dihedral_angle_1_deg 5.233 r_scangle_other 5.229 r_scbond_it 3.676 r_scbond_other 3.675 r_mcangle_it 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.573 r_dihedral_angle_4_deg 18.102 r_dihedral_angle_3_deg 13.777 r_long_range_B_refined 5.871 r_long_range_B_other 5.844 r_dihedral_angle_1_deg 5.233 r_scangle_other 5.229 r_scbond_it 3.676 r_scbond_other 3.675 r_mcangle_it 2.842 r_mcangle_other 2.841 r_mcbond_it 2.072 r_mcbond_other 2.071 r_angle_refined_deg 1.516 r_angle_other_deg 0.976 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4335 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 62
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling