3KNR

Bacillus cereus metallo-beta-lactamase Cys221Asp mutant, 1 mM Zn(II)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.92930.1 M Sodium Acetate, 2.8 M Ammonium Sulfate, 1 mM Zinc Sulfate, pH 4.9, Vapor diffusion, hanging drop., temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.143α = 90
b = 94.364β = 120.11
c = 79.898γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.421LNLSD03B-MX1

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
11.769.3496.80.04314.23.1109252
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)
11.71.7678.60.3862.7

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 REPLACEMENTTHROUGHOUT1.7123.3103745548798.050.173510.171570.21043RANDOM16.725
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]
-0.170.41-0.040.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_4_deg17.641
r_dihedral_angle_3_deg13.168
r_sphericity_free11.31
r_dihedral_angle_1_deg6.788
r_scangle_it4.979
r_scbond_it3.118
r_mcangle_it2.047
r_angle_refined_deg1.793
r_angle_other_deg1.666
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_4_deg17.641
r_dihedral_angle_3_deg13.168
r_sphericity_free11.31
r_dihedral_angle_1_deg6.788
r_scangle_it4.979
r_scbond_it3.118
r_mcangle_it2.047
r_angle_refined_deg1.793
r_angle_other_deg1.666
r_mcbond_it1.174
r_mcbond_other0.354
r_chiral_restr0.118
r_bond_refined_d0.02
r_gen_planes_refined0.009
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_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6500
Nucleic Acid Atoms
Solvent Atoms1147
Heterogen Atoms55

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction