2JFG

Crystal structure of MurD ligase in complex with UMA and ADP


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
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.085α = 90
b = 65.085β = 90
c = 134.253γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray288CCDADSC CCD2006-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.526596.30.04314.6823853
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)
11.521.6191.50.35.74.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3UAG1.5265.0980009428798.60.1890.1880.215RANDOM14.98
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]
0.080.08-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.377
r_dihedral_angle_4_deg16.232
r_dihedral_angle_3_deg11.032
r_dihedral_angle_1_deg5.82
r_scangle_it2.968
r_scbond_it1.887
r_angle_refined_deg1.59
r_mcangle_it1.258
r_mcbond_it0.696
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.377
r_dihedral_angle_4_deg16.232
r_dihedral_angle_3_deg11.032
r_dihedral_angle_1_deg5.82
r_scangle_it2.968
r_scbond_it1.887
r_angle_refined_deg1.59
r_mcangle_it1.258
r_mcbond_it0.696
r_nbtor_refined0.304
r_nbd_refined0.2
r_symmetry_hbond_refined0.17
r_symmetry_vdw_refined0.142
r_xyhbond_nbd_refined0.134
r_chiral_restr0.086
r_bond_refined_d0.043
r_gen_planes_refined0.005
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 Atoms3305
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing