☰ Navigation Tabs
Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS) IN COMPLEX WITH ~{N}-(3-azanyl-3-oxidanylidene-propyl)-5-(1-benzothiophen-5-yl)-1-(phenylmethyl)-~{N}-[(4-propan-2-yloxyphenyl)methyl]pyrazole-4-carboxamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.1M sodium cacodylate, pH 6.4, 0.12-0.24M sodium acetate.
crystals were soaked overnight in mother liquor containing 5-10mM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.451 α = 90 b = 117.911 β = 90 c = 179.693 γ = 90
Symmetry Space Group I 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 2011-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 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 2.6 50 87.3 30.7 4.5 17199
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 2.63 50 18074 979 98.85 0.2417 0.23994 0.2396 0.27421 0.2769 RANDOM 64.764
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] 1.97 -0.96 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.514 r_dihedral_angle_3_deg 12.052 r_dihedral_angle_4_deg 9.229 r_dihedral_angle_1_deg 4.815 r_angle_refined_deg 0.863 r_scangle_it 0.797 r_angle_other_deg 0.754 r_mcangle_it 0.589 r_scbond_it 0.479 r_mcbond_it 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.514 r_dihedral_angle_3_deg 12.052 r_dihedral_angle_4_deg 9.229 r_dihedral_angle_1_deg 4.815 r_angle_refined_deg 0.863 r_scangle_it 0.797 r_angle_other_deg 0.754 r_mcangle_it 0.589 r_scbond_it 0.479 r_mcbond_it 0.321 r_chiral_restr 0.045 r_mcbond_other 0.03 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3546 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing