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Cupin protein GloB from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Manually generated AlphaFold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 50 mM Tris pH 8.5, 24% PEG 8000, 0.2 M Magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.788 α = 94.176 b = 46.761 β = 91.61 c = 63.619 γ = 118.887
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 PILATUS 2M 2021-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.48 40.75 90.4 0.106 0.15 0.992 4.22 1.7 67791 22.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.57 79.4 1.34 1.897 0.223 0.5 1.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.48 40.743 67791 2084 90.401 0.22 0.2188 0.2213 0.2448 0.2486 RANDOM 20.55
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] -0.333 -0.485 0.115 -0.649 0.196 1.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.29 r_dihedral_angle_3_deg 9.838 r_lrange_it 6.509 r_dihedral_angle_1_deg 6.503 r_lrange_other 6.436 r_dihedral_angle_2_deg 5.215 r_scangle_it 4.839 r_scangle_other 4.838 r_scbond_it 2.983 r_scbond_other 2.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.29 r_dihedral_angle_3_deg 9.838 r_lrange_it 6.509 r_dihedral_angle_1_deg 6.503 r_lrange_other 6.436 r_dihedral_angle_2_deg 5.215 r_scangle_it 4.839 r_scangle_other 4.838 r_scbond_it 2.983 r_scbond_other 2.982 r_mcangle_it 2.797 r_mcangle_other 2.796 r_mcbond_it 1.81 r_mcbond_other 1.809 r_angle_refined_deg 1.286 r_angle_other_deg 0.437 r_symmetry_nbd_other 0.197 r_nbd_other 0.193 r_nbd_refined 0.184 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_3 0.072 r_ncsr_local_group_5 0.067 r_ncsr_local_group_4 0.066 r_ncsr_local_group_2 0.065 r_chiral_restr 0.058 r_ncsr_local_group_6 0.042 r_ncsr_local_group_1 0.03 r_metal_ion_refined 0.013 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3804 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing ARP/wARP model building