3MFD

The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.2M ammonium citrate tribasic pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8356.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.439α = 90
b = 100.439β = 90
c = 171.853γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-10-12MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97948, 0.97923APS19-BM

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
11.755098.60.1079.315.38790487904-3
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)
11.751.7885.30.88410.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.7534.7788772983341438898.470.165830.164560.19014RANDOM15.672
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]
0.910.91-1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.947
r_dihedral_angle_4_deg14.076
r_dihedral_angle_3_deg12.82
r_dihedral_angle_1_deg6.075
r_scangle_it3.742
r_scbond_it2.41
r_angle_refined_deg1.393
r_mcangle_it1.343
r_angle_other_deg0.852
r_mcbond_it0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.947
r_dihedral_angle_4_deg14.076
r_dihedral_angle_3_deg12.82
r_dihedral_angle_1_deg6.075
r_scangle_it3.742
r_scbond_it2.41
r_angle_refined_deg1.393
r_mcangle_it1.343
r_angle_other_deg0.852
r_mcbond_it0.75
r_mcbond_other0.232
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4958
Nucleic Acid Atoms
Solvent Atoms773
Heterogen Atoms84

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building