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The Crystal Structure of EHMT1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 25% PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.113 α = 90 b = 94.638 β = 112.337 c = 88.731 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95355 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.35 48.415 88 0.256 5.9 4.7 16513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.35 3.62 0.832
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 FREE R-VALUE 3.35 48.415 16499 798 87.264 0.198 0.1953 0.2004 0.2623 0.2556 80.887
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] 3.757 4.002 -6.696 -0.261
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 14.035 r_lrange_other 14.035 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_6_deg 11.743 r_dihedral_angle_other_3_deg 9.053 r_scangle_it 8.052 r_scangle_other 8.036 r_mcangle_it 8.012 r_mcangle_other 8.011 r_dihedral_angle_1_deg 6.595
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 14.035 r_lrange_other 14.035 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_6_deg 11.743 r_dihedral_angle_other_3_deg 9.053 r_scangle_it 8.052 r_scangle_other 8.036 r_mcangle_it 8.012 r_mcangle_other 8.011 r_dihedral_angle_1_deg 6.595 r_dihedral_angle_2_deg 5.182 r_scbond_it 4.913 r_scbond_other 4.9 r_mcbond_it 4.871 r_mcbond_other 4.871 r_dihedral_angle_other_2_deg 2.16 r_angle_refined_deg 1.086 r_symmetry_xyhbond_nbd_refined 0.396 r_angle_other_deg 0.359 r_nbd_other 0.249 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.204 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.166 r_ncsr_local_group_2 0.094 r_ncsr_local_group_1 0.091 r_ncsr_local_group_5 0.087 r_ncsr_local_group_4 0.084 r_ncsr_local_group_3 0.082 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_6 0.077 r_xyhbond_nbd_other 0.051 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8131 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing