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Crystal structure of polyprenyl diphosphate synthase A1S_2732 (Target EFI-509223) from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JYX PDB ENTRY 4JYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 294 0.5 M potassium thiocyanate, pH 4.5, 0.1 M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.245 α = 90 b = 46.008 β = 90 c = 49.286 γ = 90
Symmetry Space Group P 21 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 RAYONIX MX225HE mirrors 2013-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.9 0.13 6.1 7.1 23096 -3
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 2.03 99.2 1.7 5.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4JYX 2 30.5 22212 745 99.91 0.20231 0.20038 0.2083 0.26609 0.2725 RANDOM 47.628
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] -3.73 5.31 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_4_deg 18.486 r_dihedral_angle_3_deg 15.841 r_long_range_B_other 14.929 r_long_range_B_refined 14.91 r_scangle_other 14.353 r_scbond_it 11.911 r_scbond_other 11.911 r_mcangle_it 11.595 r_mcangle_other 11.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_4_deg 18.486 r_dihedral_angle_3_deg 15.841 r_long_range_B_other 14.929 r_long_range_B_refined 14.91 r_scangle_other 14.353 r_scbond_it 11.911 r_scbond_other 11.911 r_mcangle_it 11.595 r_mcangle_other 11.592 r_mcbond_other 10.037 r_mcbond_it 10.034 r_dihedral_angle_1_deg 4.78 r_angle_refined_deg 0.958 r_angle_other_deg 0.725 r_chiral_restr 0.049 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2494 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 9
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling