6B91

Crystal structure of the N-terminal domain of human METTL16


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H00 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.3 M K2HPO4, 45 mM NaH2PO4; drop contained 4 uL of protein solution (27 mg/mL) and 2 uL of reservoir solution, 25% ethylene glycol was used for cryo-protection
Crystal Properties
Matthews coefficientSolvent content
4.6673.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 190.05α = 90
b = 190.05β = 90
c = 190.05γ = 90
Symmetry
Space GroupI 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.945099.70.0670.0690.992516.243441
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.942.0598.21.371.420.72214.2

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 REPLACEMENTFREE R-VALUE2h001.9447.5142441100099.70.1820.1810.21RANDOM48.654
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.886
r_dihedral_angle_4_deg17.715
r_dihedral_angle_3_deg14.907
r_long_range_B_refined7.817
r_long_range_B_other7.816
r_dihedral_angle_1_deg6.339
r_scangle_other3.781
r_mcangle_other2.752
r_mcangle_it2.75
r_scbond_it2.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.886
r_dihedral_angle_4_deg17.715
r_dihedral_angle_3_deg14.907
r_long_range_B_refined7.817
r_long_range_B_other7.816
r_dihedral_angle_1_deg6.339
r_scangle_other3.781
r_mcangle_other2.752
r_mcangle_it2.75
r_scbond_it2.481
r_scbond_other2.481
r_mcbond_it1.706
r_mcbond_other1.701
r_angle_refined_deg1.624
r_angle_other_deg1.019
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2142
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
ARP/wARPmodel building