5KD2

BT_4244 metallopeptidase from Bacteroides thetaiotaomicron


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291PEG 3350, K/Na Tartrate, Tris-HCl pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.5952.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.957α = 90
b = 81.957β = 90
c = 182.138γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97945SSRLBL12-2

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
12.1570.9899.90.0715.96.539361
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)
12.152.221000.3664.16.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1570.9837472183499.840.170770.168810.20984RANDOM36.156
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]
0.720.360.72-2.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.325
r_dihedral_angle_4_deg16.16
r_dihedral_angle_3_deg13.651
r_dihedral_angle_1_deg6.655
r_long_range_B_refined5.932
r_long_range_B_other5.821
r_scangle_other4.502
r_mcangle_it3.296
r_mcangle_other3.296
r_scbond_it2.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.325
r_dihedral_angle_4_deg16.16
r_dihedral_angle_3_deg13.651
r_dihedral_angle_1_deg6.655
r_long_range_B_refined5.932
r_long_range_B_other5.821
r_scangle_other4.502
r_mcangle_it3.296
r_mcangle_other3.296
r_scbond_it2.975
r_scbond_other2.974
r_mcbond_it2.312
r_mcbond_other2.311
r_angle_refined_deg1.528
r_angle_other_deg0.816
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4796
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing