5ZJ7

Crystal structure of NDM-1 in complex with D-captopril derivative CY22


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q6X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52950.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline
Crystal Properties
Matthews coefficientSolvent content
2.0238.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.442α = 90
b = 59.964β = 98
c = 41.998γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97930SSRFBL17U1

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
10.965096.50.06721.16.2119552
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)
10.960.9969.80.3963

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3Q6X0.9641.59101895535587.540.11590.11510.1312RANDOM21.76
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]
-0.13-0.890.73-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.685
r_sphericity_free19.297
r_dihedral_angle_4_deg17.372
r_dihedral_angle_3_deg11.494
r_sphericity_bonded7.323
r_dihedral_angle_1_deg6.444
r_angle_refined_deg1.354
r_rigid_bond_restr1.033
r_angle_other_deg0.932
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.685
r_sphericity_free19.297
r_dihedral_angle_4_deg17.372
r_dihedral_angle_3_deg11.494
r_sphericity_bonded7.323
r_dihedral_angle_1_deg6.444
r_angle_refined_deg1.354
r_rigid_bond_restr1.033
r_angle_other_deg0.932
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1702
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms36

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing