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Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium
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 298 27% PEG 3350, 200 mM NaCl, 1.5 mM cholalic acid sodium salt, 100 mM
imidazole
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.296 α = 90 b = 85.711 β = 90 c = 112.558 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2017-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 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 2.097 39.443 99.6 0.107 0.113 0.035 0.998 16 9.9 28065
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 2.1 2.16 0.579 0.614 0.198 0.926 9.2
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 FREE R-VALUE 2.097 39.443 28008 1384 99.46 0.197 0.1954 0.2063 0.2362 0.2466 0.05 25.821
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] -3.088 2.935 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.069 r_dihedral_angle_6_deg 14.227 r_dihedral_angle_2_deg 6.302 r_lrange_it 5.829 r_lrange_other 5.739 r_dihedral_angle_1_deg 5.104 r_scangle_it 4.488 r_scangle_other 4.488 r_scbond_it 2.909 r_scbond_other 2.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.069 r_dihedral_angle_6_deg 14.227 r_dihedral_angle_2_deg 6.302 r_lrange_it 5.829 r_lrange_other 5.739 r_dihedral_angle_1_deg 5.104 r_scangle_it 4.488 r_scangle_other 4.488 r_scbond_it 2.909 r_scbond_other 2.909 r_mcangle_it 2.671 r_mcangle_other 2.671 r_mcbond_it 1.812 r_mcbond_other 1.81 r_angle_refined_deg 1.356 r_angle_other_deg 0.444 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.206 r_xyhbond_nbd_refined 0.197 r_nbd_other 0.186 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.176 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.064 r_metal_ion_refined 0.037 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 3486 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing