2QDS

Crystal Structure of the Zinc Carbapenemase CPHA in Complex with the Inhibitor D-Captopril


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X8G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5281PEG, AS, PH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.001α = 90
b = 100.99β = 90
c = 116.819γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.93100ESRFBM30A

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
11.6658.4199.10.0810.08117.15.73027022
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)
11.661.7594.30.2220.2224.43.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1X8G1.6650223027028699153099.080.150.149020.147910.17RANDOM12.02
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.457
r_dihedral_angle_4_deg16.396
r_dihedral_angle_3_deg11.359
r_dihedral_angle_1_deg6.014
r_scangle_it3.067
r_scbond_it1.956
r_angle_refined_deg1.283
r_mcangle_it1.141
r_angle_other_deg0.896
r_mcbond_it0.691
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.457
r_dihedral_angle_4_deg16.396
r_dihedral_angle_3_deg11.359
r_dihedral_angle_1_deg6.014
r_scangle_it3.067
r_scbond_it1.956
r_angle_refined_deg1.283
r_mcangle_it1.141
r_angle_other_deg0.896
r_mcbond_it0.691
r_nbd_refined0.364
r_symmetry_vdw_other0.317
r_nbd_other0.196
r_nbtor_refined0.181
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.158
r_mcbond_other0.157
r_symmetry_vdw_refined0.097
r_nbtor_other0.084
r_chiral_restr0.071
r_metal_ion_refined0.047
r_bond_refined_d0.01
r_bond_other_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1758
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms47

Software

Software
Software NamePurpose
CCP4model building
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing