5ZGI

Crystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule per asymmetric unit


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1M sodium succinate pH6.5, 40% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0239.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.445α = 90
b = 59.805β = 97.73
c = 42.132γ = 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
10.985093.50.09512.77.8109068
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)
10.981.0274.10.296.1

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 REPLACEMENTTHROUGHOUT3Q6X0.9841.75103572546293.550.12040.11960.1352RANDOM9.824
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]
-0.06-0.09-0.240.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.721
r_sphericity_free22.25
r_dihedral_angle_4_deg19.767
r_dihedral_angle_3_deg11.818
r_sphericity_bonded7.466
r_dihedral_angle_1_deg6.219
r_rigid_bond_restr2.445
r_angle_refined_deg1.188
r_angle_other_deg0.86
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.721
r_sphericity_free22.25
r_dihedral_angle_4_deg19.767
r_dihedral_angle_3_deg11.818
r_sphericity_bonded7.466
r_dihedral_angle_1_deg6.219
r_rigid_bond_restr2.445
r_angle_refined_deg1.188
r_angle_other_deg0.86
r_chiral_restr0.074
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1697
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms31

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing