☰ Navigation Tabs
Catalytic domain of N1484 E121S variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9XV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.26M ammonium sulfate, 0.1M HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.23 44.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.463 α = 89.97 b = 43.941 β = 90.02 c = 84.151 γ = 87.8
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 2025-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.63 28.05 95.2 0.143 0.989 10.9 3.5 57576
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.699 0.523 0.711 3.1
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 1.64 28.05 54856 2888 94.83 0.17394 0.17128 0.1874 0.22517 0.202 RANDOM 11.776
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] 1.07 -0.69 0.45 -0.64 0.06 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.786 r_long_range_B_refined 8.55 r_long_range_B_other 8.128 r_dihedral_angle_2_deg 7.192 r_dihedral_angle_1_deg 6.989 r_scangle_other 2.258 r_scbond_it 1.528 r_scbond_other 1.528 r_angle_refined_deg 1.404 r_mcangle_it 1.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.786 r_long_range_B_refined 8.55 r_long_range_B_other 8.128 r_dihedral_angle_2_deg 7.192 r_dihedral_angle_1_deg 6.989 r_scangle_other 2.258 r_scbond_it 1.528 r_scbond_other 1.528 r_angle_refined_deg 1.404 r_mcangle_it 1.394 r_mcangle_other 1.394 r_mcbond_it 0.882 r_mcbond_other 0.881 r_angle_other_deg 0.48 r_chiral_restr 0.07 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3830 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction