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Structure of the Y108F mutant of vanillyl alcohol oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 PEG4000, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.9 α = 90 b = 137.9 β = 90 c = 132.9 γ = 90
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-F 2015-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.71, 2.25 SLS X06DA
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 2.5 54.91 89.7 0.098 0.077 0.985 9 2.3 62110 27138
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.8 91.9 0.711 0.58 0.539 1.3 2.1 8772
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) 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 2VAO 2.8 54.91 25824 1309 88.56 0.18383 0.17997 0.1857 0.2586 0.2538 RANDOM 52.058
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] 1.74 1.74 -3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.847 r_dihedral_angle_3_deg 18.63 r_dihedral_angle_4_deg 18.39 r_dihedral_angle_1_deg 7.402 r_long_range_B_refined 6.837 r_long_range_B_other 6.836 r_mcangle_it 4.521 r_mcangle_other 4.52 r_scangle_other 4.22 r_mcbond_it 2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.847 r_dihedral_angle_3_deg 18.63 r_dihedral_angle_4_deg 18.39 r_dihedral_angle_1_deg 7.402 r_long_range_B_refined 6.837 r_long_range_B_other 6.836 r_mcangle_it 4.521 r_mcangle_other 4.52 r_scangle_other 4.22 r_mcbond_it 2.805 r_mcbond_other 2.805 r_scbond_it 2.575 r_scbond_other 2.574 r_angle_refined_deg 1.561 r_angle_other_deg 1.018 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8697 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing