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Crystal structure of alcohol oxidase PaAox1 from Picea abies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298.15 0.2 M CaCl2
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.099 α = 90 b = 99.273 β = 100.249 c = 87.959 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS EIGER2 XE 16M 2023-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.64 65.24 94.6 0.119 0.05 0.997 10.5 6.3 123313
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 61.9 1.802 0.33
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 1.64 65.24 122933 6243 94.285 0.186 0.1851 0.185 0.2096 0.2098 29.154
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] -0.001 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.318 r_dihedral_angle_3_deg 12.084 r_dihedral_angle_2_deg 8.084 r_lrange_it 7.491 r_dihedral_angle_1_deg 7.041 r_scangle_it 6.274 r_scbond_it 4.173 r_mcangle_it 3.692 r_mcbond_it 2.635 r_angle_refined_deg 1.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.318 r_dihedral_angle_3_deg 12.084 r_dihedral_angle_2_deg 8.084 r_lrange_it 7.491 r_dihedral_angle_1_deg 7.041 r_scangle_it 6.274 r_scbond_it 4.173 r_mcangle_it 3.692 r_mcbond_it 2.635 r_angle_refined_deg 1.771 r_nbtor_refined 0.309 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.162 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.132 r_symmetry_xyhbond_nbd_refined 0.125 r_ncsr_local_group_1 0.087 r_metal_ion_refined 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7437 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 271
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing