4QJG

Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin V


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JBF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52920.2 M NaCl, 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.6253.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.723α = 90
b = 70.019β = 96.93
c = 114.625γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2013-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.853099.80.0717.73.88928989289-336.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8897.70.462.73.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4JBF1.85308484684846442399.580.176310.174790.20568RANDOM36.064
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]
4.262.13-3.57-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.776
r_dihedral_angle_3_deg10.987
r_dihedral_angle_4_deg10.486
r_long_range_B_refined8.009
r_long_range_B_other7.911
r_scangle_other5.741
r_scbond_it4.19
r_scbond_other4.189
r_mcangle_it3.849
r_mcangle_other3.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.776
r_dihedral_angle_3_deg10.987
r_dihedral_angle_4_deg10.486
r_long_range_B_refined8.009
r_long_range_B_other7.911
r_scangle_other5.741
r_scbond_it4.19
r_scbond_other4.189
r_mcangle_it3.849
r_mcangle_other3.849
r_dihedral_angle_1_deg3.316
r_mcbond_it2.731
r_mcbond_other2.729
r_angle_refined_deg1.82
r_angle_other_deg0.894
r_chiral_restr0.108
r_gen_planes_refined0.018
r_bond_refined_d0.014
r_gen_planes_other0.014
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms6012
Nucleic Acid Atoms
Solvent Atoms580
Heterogen Atoms48

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling