5O2F

Crystal structure of NDM-1 in complex with hydrolyzed ampicillin - new refinement


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829528% (w/v) PEG3350, 0.1 M Bis-Tris, pH 5.8 and 0.2 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.935.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.62α = 90
b = 77.57β = 90
c = 132.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.00838.78599.426843

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 REPLACEMENTTHROUGHOUT3q6x2.0138.78525437134597.710.134510.131920.18216RANDOM20.341
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]
1.9-1.52-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.418
r_dihedral_angle_4_deg19.261
r_dihedral_angle_3_deg13.195
r_dihedral_angle_1_deg6.204
r_long_range_B_other5.858
r_long_range_B_refined5.857
r_sphericity_bonded5.272
r_scangle_other4.075
r_scbond_it2.636
r_scbond_other2.633
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.418
r_dihedral_angle_4_deg19.261
r_dihedral_angle_3_deg13.195
r_dihedral_angle_1_deg6.204
r_long_range_B_other5.858
r_long_range_B_refined5.857
r_sphericity_bonded5.272
r_scangle_other4.075
r_scbond_it2.636
r_scbond_other2.633
r_mcangle_other2.221
r_mcangle_it2.219
r_mcbond_it1.544
r_mcbond_other1.541
r_angle_refined_deg1.453
r_angle_other_deg0.959
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3620
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling
PHASESphasing