☰ Navigation Tabs
K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22 % PEG 3,350, 6 % Tacsimate pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.462 α = 106.15 b = 90.189 β = 105.49 c = 104.224 γ = 107.47
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 RAYONIX MX-300 2022-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.976 APS 21-ID-F
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 2.4 43.11 93.3 0.997 8.1 3.8 100667
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 2.4 2.44 0.933
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 43.11 94925 4883 92.5 0.21206 0.21044 0.2141 0.24295 0.2428 RANDOM 41.643
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] 3.27 1.32 -6.11 2.51 -5.77 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.316 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 18.823 r_long_range_B_refined 9.881 r_long_range_B_other 9.88 r_dihedral_angle_1_deg 7.406 r_scangle_other 6.997 r_mcangle_it 6.586 r_mcangle_other 6.586 r_scbond_it 4.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.316 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 18.823 r_long_range_B_refined 9.881 r_long_range_B_other 9.88 r_dihedral_angle_1_deg 7.406 r_scangle_other 6.997 r_mcangle_it 6.586 r_mcangle_other 6.586 r_scbond_it 4.482 r_scbond_other 4.482 r_mcbond_it 4.255 r_mcbond_other 4.25 r_angle_refined_deg 1.666 r_angle_other_deg 1.315 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16059 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 348
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing