☰ Navigation Tabs
Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151N mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.2 M NaCl and 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.525 α = 90 b = 142.426 β = 90 c = 286.436 γ = 90
Symmetry Space Group C 2 2 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 2M 2022-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.999870 ESRF MASSIF-1
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 2.1 143.22 100 0.139 0.143 0.032 0.999 14.3 20.1 106762
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 2.14 100 2.349 2.407 0.526 0.553 20.7
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 (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 2.1 143.22 101143 5544 99.96 0.18655 0.18409 0.194 0.23168 0.2336 RANDOM 48.684
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] -0.14 1.17 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.49 r_long_range_B_refined 7.651 r_long_range_B_other 7.648 r_dihedral_angle_2_deg 7.198 r_dihedral_angle_1_deg 7.147 r_scangle_other 6.299 r_mcangle_it 4.819 r_mcangle_other 4.819 r_scbond_it 4.349 r_scbond_other 4.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.49 r_long_range_B_refined 7.651 r_long_range_B_other 7.648 r_dihedral_angle_2_deg 7.198 r_dihedral_angle_1_deg 7.147 r_scangle_other 6.299 r_mcangle_it 4.819 r_mcangle_other 4.819 r_scbond_it 4.349 r_scbond_other 4.349 r_mcbond_it 3.705 r_mcbond_other 3.704 r_angle_refined_deg 1.369 r_angle_other_deg 0.463 r_chiral_restr 0.064 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 12241 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing