5KH5 | pdb_00005kh5

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2980.1M 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 coefficientSolvent content
2.5551.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.451α = 90
b = 117.911β = 90
c = 179.693γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2011-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.65087.330.74.517199

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.63501807497998.850.24170.239940.240.274210.28RANDOM64.764
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.514
r_dihedral_angle_3_deg12.052
r_dihedral_angle_4_deg9.229
r_dihedral_angle_1_deg4.815
r_angle_refined_deg0.863
r_scangle_it0.797
r_angle_other_deg0.754
r_mcangle_it0.589
r_scbond_it0.479
r_mcbond_it0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.514
r_dihedral_angle_3_deg12.052
r_dihedral_angle_4_deg9.229
r_dihedral_angle_1_deg4.815
r_angle_refined_deg0.863
r_scangle_it0.797
r_angle_other_deg0.754
r_mcangle_it0.589
r_scbond_it0.479
r_mcbond_it0.321
r_chiral_restr0.045
r_mcbond_other0.03
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3546
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing