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Crystal structure of NTMT1 in complex with N-terminally methylated PPKRIA peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other isomorphous structure of NTMT1 in complex with different peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 26% PEG3350, 16% tacsimate
Crystal Properties Matthews coefficient Solvent content 3.06 59.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.268 α = 90 b = 107.268 β = 90 c = 205.604 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 2015-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 29.65 99.2 0.13 0.133 0.028 0.999 27.7 21.1 64736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 98 1.18 1.208 0.257 0.87 3.6 21.1 3713
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT isomorphous structure of NTMT1 in complex with different peptide 1.95 29.65 49282 2019 99.31 0.1537 0.1524 0.1875 0.1672 THIN SHELLS (SFTOOLS) 18.6
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] 0.14 0.07 0.14 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.292 r_dihedral_angle_4_deg 18.934 r_dihedral_angle_3_deg 12.196 r_dihedral_angle_1_deg 6.172 r_angle_refined_deg 1.766 r_angle_other_deg 1.339 r_mcangle_it 0.913 r_mcbond_it 0.539 r_mcbond_other 0.533 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.292 r_dihedral_angle_4_deg 18.934 r_dihedral_angle_3_deg 12.196 r_dihedral_angle_1_deg 6.172 r_angle_refined_deg 1.766 r_angle_other_deg 1.339 r_mcangle_it 0.913 r_mcbond_it 0.539 r_mcbond_other 0.533 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3642 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 115
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction