5ZGW

Crystal structure of NDM-1 at pH7.5 with 1 molecule per asymmetric unit (crystallized at succinate pH5.5 and soaked at succinate pH7.5)


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 sodium succinate pH5.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
238.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.456α = 90
b = 59.905β = 98.14
c = 41.74γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-03-27MSINGLE 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
10.955098.70.10810.67.1125133
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)
10.950.9896.10.3253.9

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 REPLACEMENTTHROUGHOUT3Q6X0.9541.32118845626698.640.12930.12870.1404RANDOM9.555
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]
-0.340.29-0.671.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.486
r_dihedral_angle_4_deg20.198
r_sphericity_free17.146
r_dihedral_angle_3_deg11.069
r_dihedral_angle_1_deg6.282
r_sphericity_bonded5.693
r_rigid_bond_restr1.739
r_angle_refined_deg1.234
r_angle_other_deg0.843
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.486
r_dihedral_angle_4_deg20.198
r_sphericity_free17.146
r_dihedral_angle_3_deg11.069
r_dihedral_angle_1_deg6.282
r_sphericity_bonded5.693
r_rigid_bond_restr1.739
r_angle_refined_deg1.234
r_angle_other_deg0.843
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1701
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms33

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing