5K4M

Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-3


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
1.9737.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.82α = 90
b = 138.16β = 90
c = 78.2γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-11-06MSINGLE 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
11.9839.1399.720.028630.99911.13214613
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)
11.9832.05499.370.08255.782

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 REPLACEMENTTHROUGHOUT3SPU1.9839.131387773699.70.144830.141540.20775RANDOM16.095
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]
-0.17-0.120.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.948
r_dihedral_angle_4_deg20.254
r_dihedral_angle_3_deg14.723
r_dihedral_angle_1_deg6.746
r_long_range_B_refined6.111
r_long_range_B_other6.109
r_scangle_other2.957
r_mcangle_it2.747
r_mcangle_other2.747
r_angle_refined_deg1.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.948
r_dihedral_angle_4_deg20.254
r_dihedral_angle_3_deg14.723
r_dihedral_angle_1_deg6.746
r_long_range_B_refined6.111
r_long_range_B_other6.109
r_scangle_other2.957
r_mcangle_it2.747
r_mcangle_other2.747
r_angle_refined_deg1.922
r_scbond_it1.894
r_scbond_other1.894
r_mcbond_it1.637
r_mcbond_other1.631
r_angle_other_deg0.947
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms187
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing