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Structure of Undecaprenyl Diphosphate synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298.15 5% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.633 α = 90 b = 68.762 β = 90 c = 111.816 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 CCD MARMOSAIC 225 mm CCD 2009-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.7 50 97.5 0.051 51.2 7.2 50646
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 1.7 1.73 99.7 0.4 3.7 5.8
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 MOLECULAR REPLACEMENT THROUGHOUT 2E99 1.7 27.95 53420 50646 2711 99.5 0.186 0.184 0.2021 0.224 0.2345 RANDOM 28.989
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] 0.07 -0.13 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.08 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 15.18 r_scangle_it 6.198 r_dihedral_angle_1_deg 5.912 r_scbond_it 3.869 r_mcangle_it 2.592 r_angle_refined_deg 2.115 r_mcbond_it 1.517 r_chiral_restr 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.08 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 15.18 r_scangle_it 6.198 r_dihedral_angle_1_deg 5.912 r_scbond_it 3.869 r_mcangle_it 2.592 r_angle_refined_deg 2.115 r_mcbond_it 1.517 r_chiral_restr 0.18 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3451 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling