2JFH | pdb_00002jfh

Crystal structure of MurD ligase in complex with L-Glu containing sulfonamide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UAGPDB ENTRY 3UAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLIZED FROM 1.7 M (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 10 MM OF INHIBITOR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
3.160

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.593α = 90
b = 65.593β = 90
c = 135.485γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray288CCDADSC CCD2006-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.865094.60.05223.7453533
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)
11.861.9787.20.2764

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3UAG1.9747.1437092195796.80.2160.2140.210.2510.25RANDOM17.07
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]
-0.16-0.160.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_4_deg15.245
r_dihedral_angle_3_deg14.025
r_dihedral_angle_1_deg5.575
r_scangle_it3.839
r_scbond_it2.642
r_angle_refined_deg1.596
r_mcangle_it1.581
r_mcbond_it0.985
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_4_deg15.245
r_dihedral_angle_3_deg14.025
r_dihedral_angle_1_deg5.575
r_scangle_it3.839
r_scbond_it2.642
r_angle_refined_deg1.596
r_mcangle_it1.581
r_mcbond_it0.985
r_nbtor_refined0.303
r_nbd_refined0.219
r_symmetry_hbond_refined0.21
r_symmetry_vdw_refined0.197
r_xyhbond_nbd_refined0.187
r_chiral_restr0.131
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms3227
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing