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Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EX4 pdbid 2ex4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 26% PEG3350, 16% tacsimate
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.16 α = 90 b = 107.16 β = 90 c = 205.589 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 1.75 29.62 100 0.125 0.129 0.028 0.999 27.6 20.8 70896
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 1.75 1.78 99.9 1.139 1.169 0.261 0.841 3.5 19.8 3828
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdbid 2ex4 1.75 29.6 68176 2626 99.93 0.1581 0.1571 0.1718 0.184 0.1948 THIN SHELLS (SFTOOLS) 17.264
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] -0.02 -0.01 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.289 r_dihedral_angle_4_deg 15.033 r_dihedral_angle_3_deg 11.527 r_dihedral_angle_1_deg 6.219 r_angle_refined_deg 1.761 r_angle_other_deg 1.034 r_mcangle_it 0.822 r_mcbond_it 0.492 r_mcbond_other 0.484 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.289 r_dihedral_angle_4_deg 15.033 r_dihedral_angle_3_deg 11.527 r_dihedral_angle_1_deg 6.219 r_angle_refined_deg 1.761 r_angle_other_deg 1.034 r_mcangle_it 0.822 r_mcbond_it 0.492 r_mcbond_other 0.484 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3638 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction