5ZGX

Crystal structure of NDM-1 at pH7.5 (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 DROP7.52950.1M sodium succinate pH7.5, 30% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0138.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.451α = 90
b = 59.885β = 97.94
c = 41.972γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-01-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.93924SSRFBL17U1

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
10.955098.60.07613.64.8125535
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)
10.950.9886.30.4853.7

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 REPLACEMENTTHROUGHOUT3q6x0.9533.88119202629798.390.11320.11260.1246RANDOM10.46
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]
-0.04-0.01-0.230.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.134
r_sphericity_free30.705
r_dihedral_angle_4_deg17.787
r_dihedral_angle_3_deg12.577
r_sphericity_bonded7.348
r_dihedral_angle_1_deg6.475
r_angle_refined_deg1.458
r_angle_other_deg1.404
r_rigid_bond_restr1.375
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.134
r_sphericity_free30.705
r_dihedral_angle_4_deg17.787
r_dihedral_angle_3_deg12.577
r_sphericity_bonded7.348
r_dihedral_angle_1_deg6.475
r_angle_refined_deg1.458
r_angle_other_deg1.404
r_rigid_bond_restr1.375
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1701
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing