5JQJ

Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.752910.1 M MES pH 6.75, 1.3 M MgSO4
Crystal Properties
Matthews coefficientSolvent content
1.9436.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.795α = 90
b = 137.724β = 90
c = 77.455γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.6734.4597.220.029290.99917.9322331819.27
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)
11.671.7377.720.461.892

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 REPLACEMENTTHROUGHOUT3SPU1.6734.4522123119597.20.146590.144360.18687RANDOM23.277
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]
-0.63-0.220.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.502
r_dihedral_angle_4_deg22.279
r_dihedral_angle_3_deg14.469
r_long_range_B_other7.455
r_long_range_B_refined7.453
r_dihedral_angle_1_deg6.419
r_scangle_other4.175
r_mcangle_it3.463
r_mcangle_other3.462
r_scbond_it2.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.502
r_dihedral_angle_4_deg22.279
r_dihedral_angle_3_deg14.469
r_long_range_B_other7.455
r_long_range_B_refined7.453
r_dihedral_angle_1_deg6.419
r_scangle_other4.175
r_mcangle_it3.463
r_mcangle_other3.462
r_scbond_it2.93
r_scbond_other2.93
r_mcbond_it2.327
r_mcbond_other2.323
r_angle_refined_deg2.075
r_angle_other_deg0.984
r_chiral_restr0.138
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.001
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
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1699
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing