5AGI | pdb_00005agi

Crystal structure of the LeuRS editing domain of Candida albicans Mutant K510A in complex with the adduct formed by AN2690-AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WFGPDB ENTRY 2WFG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.40.2 M SODIUM ACETATE, 0.1 M HEPES SODIUM PH 7.4, 30% PEG 2000
Crystal Properties
Matthews coefficientSolvent content
1.9938.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.176α = 90
b = 58.427β = 90
c = 95.163γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-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
11.4749.7999.30.0737.49.1385172
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)
11.471.5191.20.54.28.8

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 2WFG1.4749.7938517203399.330.199940.198990.210.21750.22RANDOM14.162
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]
-0.250.140.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.912
r_sphericity_free15.862
r_dihedral_angle_3_deg11.227
r_dihedral_angle_4_deg7.828
r_sphericity_bonded4.965
r_dihedral_angle_1_deg4.604
r_angle_refined_deg1.192
r_rigid_bond_restr1.036
r_angle_other_deg0.67
r_mcangle_it0.452
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.912
r_sphericity_free15.862
r_dihedral_angle_3_deg11.227
r_dihedral_angle_4_deg7.828
r_sphericity_bonded4.965
r_dihedral_angle_1_deg4.604
r_angle_refined_deg1.192
r_rigid_bond_restr1.036
r_angle_other_deg0.67
r_mcangle_it0.452
r_scbond_it0.435
r_mcbond_it0.38
r_mcbond_other0.379
r_chiral_restr0.114
r_bond_refined_d0.004
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_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1986
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing