5YJF

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82950.2M Sodium chloride, 0.1M BIS-TRIS pH 5.8, 25 %(w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.8934.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.323α = 90
b = 132.976β = 103.57
c = 61.317γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152016-12-07MSINGLE 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
12.4847.7896.45.76.431948
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)
12.480.8850.411

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 REPLACEMENTTHROUGHOUT3ROD2.4947.7830164161796.30.226930.223740.28553RANDOM34.075
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]
-2.64-0.381.451.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg17.984
r_dihedral_angle_1_deg6.15
r_scangle_it1.671
r_angle_refined_deg1.294
r_scbond_it1.022
r_mcangle_it0.674
r_mcbond_it0.377
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg17.984
r_dihedral_angle_1_deg6.15
r_scangle_it1.671
r_angle_refined_deg1.294
r_scbond_it1.022
r_mcangle_it0.674
r_mcbond_it0.377
r_nbtor_refined0.305
r_symmetry_vdw_refined0.23
r_symmetry_hbond_refined0.215
r_nbd_refined0.213
r_xyhbond_nbd_refined0.154
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms7873
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing