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Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2 ul protein (9.5mg/ml in 50mM Tris-HCl, pH 7.5, 0.2M NaCl, 1mM EDTA) mixed with 2ul reservoir solution containing either 10-20% ethanol, 0.1M Tris-Hcl, pH 8.5 or 4-5% PEG 6000, 0.1M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.687 α = 90 b = 118.029 β = 90 c = 178.326 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 100 CCD MARRESEARCH 1999-11-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.987,1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 94.3 15 5 53529
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.3 20 52056 2792 91.62 0.21418 0.21255 0.2122 0.24491 0.2441 RANDOM 42.672
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 0.38 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.47 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_4_deg 11.544 r_dihedral_angle_1_deg 5.304 r_long_range_B_refined 4.579 r_long_range_B_other 4.451 r_angle_refined_deg 1.099 r_mcangle_it 1.069 r_mcangle_other 1.069 r_angle_other_deg 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.47 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_4_deg 11.544 r_dihedral_angle_1_deg 5.304 r_long_range_B_refined 4.579 r_long_range_B_other 4.451 r_angle_refined_deg 1.099 r_mcangle_it 1.069 r_mcangle_other 1.069 r_angle_other_deg 0.857 r_scangle_other 0.597 r_mcbond_it 0.568 r_mcbond_other 0.568 r_scbond_it 0.292 r_scbond_other 0.292 r_chiral_restr 0.057 r_bond_refined_d 0.007 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 6856 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing