☰ Navigation Tabs
Escherichia coli OpgD mutant-D388N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG2000MME, TMAO, tris-HCl (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 4.71 73.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.75 α = 90 b = 392.76 β = 90 c = 324.648 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS3 S 6M 2022-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.95 49.143 100 0.208 0.994 13 13.7 301232
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 2.95 3 0.869
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 2.95 49.143 301231 14722 99.939 0.196 0.1937 0.198 0.2322 0.2326 34.688
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] -1.584 -0.932 2.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.722 r_dihedral_angle_4_deg 20.014 r_dihedral_angle_3_deg 18.449 r_dihedral_angle_1_deg 7.239 r_lrange_other 7.182 r_lrange_it 7.181 r_scangle_it 5.028 r_scangle_other 5.028 r_mcangle_other 4.337 r_mcangle_it 4.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.722 r_dihedral_angle_4_deg 20.014 r_dihedral_angle_3_deg 18.449 r_dihedral_angle_1_deg 7.239 r_lrange_other 7.182 r_lrange_it 7.181 r_scangle_it 5.028 r_scangle_other 5.028 r_mcangle_other 4.337 r_mcangle_it 4.336 r_scbond_it 3.149 r_scbond_other 3.149 r_mcbond_it 2.733 r_mcbond_other 2.733 r_angle_other_deg 2.332 r_angle_refined_deg 1.602 r_symmetry_nbd_refined 0.266 r_nbd_other 0.248 r_symmetry_nbd_other 0.232 r_nbd_refined 0.21 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_other 0.11 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.065 r_bond_other_d 0.035 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 50952 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing