5CXW

Structure of the PonA1 protein from Mycobacterium Tuberculosis in complex with penicillin V


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CRF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52920.1 M HEPES, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.341α = 90
b = 60.58β = 90
c = 133.904γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-11-24MSINGLE 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
11.753099.50.09823.57.239656
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)
11.751.78990.6343.17.1

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 REPLACEMENTTHROUGHOUT5CRF1.753037678192199.440.148950.146920.18937RANDOM20.069
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]
0.93-0.44-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.867
r_dihedral_angle_3_deg12.857
r_dihedral_angle_4_deg10.775
r_long_range_B_refined5.922
r_long_range_B_other5.922
r_dihedral_angle_1_deg5.553
r_scangle_other2.087
r_angle_refined_deg1.719
r_mcangle_it1.526
r_mcangle_other1.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.867
r_dihedral_angle_3_deg12.857
r_dihedral_angle_4_deg10.775
r_long_range_B_refined5.922
r_long_range_B_other5.922
r_dihedral_angle_1_deg5.553
r_scangle_other2.087
r_angle_refined_deg1.719
r_mcangle_it1.526
r_mcangle_other1.526
r_scbond_it1.291
r_scbond_other1.288
r_angle_other_deg0.99
r_mcbond_it0.896
r_mcbond_other0.895
r_chiral_restr0.125
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2742
Nucleic Acid Atoms
Solvent Atoms456
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing