☰ Navigation Tabs
Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 30% PEG 4,000, 200 mM MgCl2, 100 mM HEPES HCl
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.192 α = 90 b = 74.33 β = 90 c = 111.953 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS PILATUS 6M 2022-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979460 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.95 37.32 100 0.059 0.061 0.017 1 26.7 13.2 17168 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.666 0.692 0.186 0.937 4.3 13.7
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 SAD FREE R-VALUE 1.95 37.165 17143 826 99.901 0.172 0.1692 0.1809 0.2167 0.2206 0.05 35.558
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] 0.004 0.018 -0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.068 r_dihedral_angle_3_deg 15.201 r_dihedral_angle_2_deg 10.147 r_lrange_it 8.901 r_lrange_other 8.894 r_scangle_it 7.761 r_scangle_other 7.758 r_dihedral_angle_1_deg 6.013 r_scbond_it 5.778 r_scbond_other 5.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.068 r_dihedral_angle_3_deg 15.201 r_dihedral_angle_2_deg 10.147 r_lrange_it 8.901 r_lrange_other 8.894 r_scangle_it 7.761 r_scangle_other 7.758 r_dihedral_angle_1_deg 6.013 r_scbond_it 5.778 r_scbond_other 5.774 r_mcangle_it 5.571 r_mcangle_other 5.569 r_mcbond_it 4.29 r_mcbond_other 4.288 r_angle_refined_deg 2.117 r_angle_other_deg 0.727 r_nbd_refined 0.234 r_symmetry_nbd_refined 0.226 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.182 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.111 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1614 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing