☰ Navigation Tabs
Structure of the Y503F 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 PEG4000, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.012 α = 90 b = 138.012 β = 90 c = 132.94 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 0.999 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 2.8 54.94 91.8 0.113 0.087 0.988 7 2.4 65596 27846
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 2.8 2.95 94.3 0.705 0.545 0.54 1.3 2.4 10160
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 54.94 26493 1353 90.69 0.17884 0.17522 0.1817 0.24886 0.2489 RANDOM 52.61
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] 1.55 1.55 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.782 r_dihedral_angle_4_deg 20.34 r_dihedral_angle_3_deg 17.979 r_dihedral_angle_1_deg 7.181 r_long_range_B_refined 6.782 r_long_range_B_other 6.779 r_mcangle_it 4.497 r_mcangle_other 4.497 r_scangle_other 4.262 r_mcbond_it 2.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.782 r_dihedral_angle_4_deg 20.34 r_dihedral_angle_3_deg 17.979 r_dihedral_angle_1_deg 7.181 r_long_range_B_refined 6.782 r_long_range_B_other 6.779 r_mcangle_it 4.497 r_mcangle_other 4.497 r_scangle_other 4.262 r_mcbond_it 2.801 r_mcbond_other 2.801 r_scbond_it 2.638 r_scbond_other 2.638 r_angle_refined_deg 1.547 r_angle_other_deg 1.013 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 8706 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing