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The structure of IpCS3, a theobromine methyltransferase from Yerba Mate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 282.15 25% PEG 3350, 0.2 M NH4SO4, 0.1 M Bis Tris methane pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.675 α = 90 b = 82.675 β = 90 c = 226.088 γ = 90
Symmetry Space Group P 41 21 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 MARMOSAIC 300 mm CCD 2021-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.72 37.001 99.9 0.999 25.79 2 21910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.82 0.878
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.721 37.001 21909 1083 99.9 0.197 0.1937 0.1937 0.2485 0.2485 63.37
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] -0.035 -0.035 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_3_deg 18.625 r_dihedral_angle_4_deg 10.968 r_lrange_it 10.247 r_scangle_it 6.889 r_dihedral_angle_1_deg 6.444 r_mcangle_it 6.415 r_scbond_it 4.487 r_mcbond_it 4.027 r_angle_refined_deg 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_3_deg 18.625 r_dihedral_angle_4_deg 10.968 r_lrange_it 10.247 r_scangle_it 6.889 r_dihedral_angle_1_deg 6.444 r_mcangle_it 6.415 r_scbond_it 4.487 r_mcbond_it 4.027 r_angle_refined_deg 1.112 r_nbtor_refined 0.307 r_symmetry_nbd_refined 0.229 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.097 r_ncsr_local_group_1 0.084 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5292 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHENIX phasing