5YJI

Co-crystal structure of Mouse Nicotinamide N-methyltransferase (NNMT) with small molecule analog of Nicotinamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.35M Sodium thiocynate, 20% PEG 3350, with 0.01M TMAO as additive
Crystal Properties
Matthews coefficientSolvent content
2.141.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.356α = 90
b = 71.622β = 90
c = 157.408γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9947.3699.614.29.537822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.990.520.182

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 REPLACEMENTTHROUGHOUT3ROD1.9947.3635850189099.590.211570.210170.23825RANDOM19.797
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]
-0.160.81-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.589
r_dihedral_angle_4_deg17.992
r_dihedral_angle_3_deg14.47
r_dihedral_angle_1_deg5.509
r_scangle_it2.05
r_scbond_it1.216
r_angle_refined_deg1.153
r_mcangle_it0.913
r_mcbond_it0.517
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.589
r_dihedral_angle_4_deg17.992
r_dihedral_angle_3_deg14.47
r_dihedral_angle_1_deg5.509
r_scangle_it2.05
r_scbond_it1.216
r_angle_refined_deg1.153
r_mcangle_it0.913
r_mcbond_it0.517
r_nbtor_refined0.3
r_symmetry_vdw_refined0.207
r_nbd_refined0.184
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.126
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3982
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing