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SbSOMT in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.04 M Citric Acid/0.06 M Bis-Tris Propane pH 6.4; 20% PEG 3350; 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.2 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.87 α = 90 b = 94.382 β = 113.713 c = 64.993 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 EIGER2 S 9M 2025-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
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 2.9 94.38 97.7 0.996 9.7 6.9 15690
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 2.9 3.08 0.656
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 2.9 59.577 15668 778 97.723 0.218 0.2165 0.2184 0.2508 0.2582 87.535
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] 1.192 0.469 -4.399 2.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.942 r_dihedral_angle_6_deg 11.458 r_lrange_it 7.643 r_lrange_other 7.643 r_dihedral_angle_1_deg 5.294 r_dihedral_angle_2_deg 3.754 r_scangle_it 3.71 r_scangle_other 3.709 r_mcangle_it 3.43 r_mcangle_other 3.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.942 r_dihedral_angle_6_deg 11.458 r_lrange_it 7.643 r_lrange_other 7.643 r_dihedral_angle_1_deg 5.294 r_dihedral_angle_2_deg 3.754 r_scangle_it 3.71 r_scangle_other 3.709 r_mcangle_it 3.43 r_mcangle_other 3.43 r_scbond_it 2.135 r_scbond_other 2.134 r_mcbond_it 2.007 r_mcbond_other 2.007 r_angle_refined_deg 0.849 r_angle_other_deg 0.322 r_nbd_refined 0.199 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.174 r_nbd_other 0.156 r_ncsr_local_group_1 0.128 r_xyhbond_nbd_refined 0.123 r_symmetry_nbd_refined 0.123 r_symmetry_xyhbond_nbd_refined 0.082 r_symmetry_nbtor_other 0.074 r_dihedral_angle_other_2_deg 0.051 r_chiral_restr 0.043 r_ext_dist_refined_b 0.042 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5550 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing autoPROC data processing Coot model building PDB-REDO refinement