3PBI

Structure of the peptidoglycan hydrolase RipB (Rv1478) from Mycobacterium tuberculosis at 1.6 resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52930.2 M NaCl 0.1 M HEPES, 30% v/v PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0759.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.98α = 90
b = 92.98β = 90
c = 53.192γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2009-10-25MSINGLE 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)R Sym 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
11.64092.30.0660.06619.17.4320632.520.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6963.20.4110.4112.52.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 2HBW1.6402.532063160492.30.1610.1590.196RANDOM19.26
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]
-0.74-0.37-0.741.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_4_deg19.803
r_dihedral_angle_3_deg13.239
r_dihedral_angle_1_deg6.277
r_scangle_it4.646
r_scbond_it2.909
r_mcangle_it2.192
r_angle_refined_deg2.076
r_mcbond_it1.459
r_angle_other_deg1.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_4_deg19.803
r_dihedral_angle_3_deg13.239
r_dihedral_angle_1_deg6.277
r_scangle_it4.646
r_scbond_it2.909
r_mcangle_it2.192
r_angle_refined_deg2.076
r_mcbond_it1.459
r_angle_other_deg1.132
r_mcbond_other0.47
r_chiral_restr0.137
r_bond_refined_d0.029
r_gen_planes_refined0.011
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1436
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling