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CO dehydrogenase 2 variant A559W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 PEG 2000MME
Crystal Properties Matthews coefficient Solvent content 2.09 41.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.31 α = 90 b = 75.33 β = 111.56 c = 71.59 γ = 90
Symmetry Space Group C 1 2 1
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 2025-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.49 40.77 99.4 0.998 9.81 3.41 175782
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 1.49 1.58 0.322
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 1.49 40.799 89567 1071 99.88 0.175 0.1749 0.1755 0.2126 0.2132 RANDOM 13.54
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] 0.576 -0.486 -1.246 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.631 r_dihedral_angle_3_deg 13.953 r_scangle_other 10.101 r_scangle_it 10.083 r_dihedral_angle_1_deg 9.322 r_lrange_other 9.212 r_lrange_it 9.194 r_scbond_other 9.012 r_scbond_it 8.97 r_mcangle_other 4.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.631 r_dihedral_angle_3_deg 13.953 r_scangle_other 10.101 r_scangle_it 10.083 r_dihedral_angle_1_deg 9.322 r_lrange_other 9.212 r_lrange_it 9.194 r_scbond_other 9.012 r_scbond_it 8.97 r_mcangle_other 4.951 r_mcangle_it 4.95 r_mcbond_it 4.306 r_mcbond_other 4.303 r_angle_refined_deg 2.048 r_angle_other_deg 0.482 r_chiral_restr 0.37 r_nbd_refined 0.223 r_symmetry_nbd_other 0.19 r_nbd_other 0.173 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.158 r_symmetry_metal_ion_refined 0.157 r_metal_ion_refined 0.151 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.082 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4663 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PHASER phasing XSCALE data scaling