☰ Navigation Tabs
F194Y mutant of the Dye-decolorizing peroxidase (DYP) from Pleurotus ostreatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.75 295 0.2M MES pH=5.75 25%PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.717 α = 90 b = 117.575 β = 90 c = 140.434 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976252 ESRF ID30B
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 1.56 70.22 97.3 0.065 0.083 0.051 0.997 12.7 4.5 144926 17.7
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 1.56 1.64 97.4 0.514 0.649 0.392 0.745 2.3 4.6
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 3AFV 1.56 70.22 137552 7250 97.05 0.16386 0.16201 0.1763 0.19885 0.21 RANDOM 18.56
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] 0.21 0.04 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_4_deg 23.237 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 6.184 r_long_range_B_refined 5.488 r_long_range_B_other 5.488 r_scangle_other 4.166 r_scbond_it 2.76 r_scbond_other 2.76 r_mcangle_it 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_4_deg 23.237 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 6.184 r_long_range_B_refined 5.488 r_long_range_B_other 5.488 r_scangle_other 4.166 r_scbond_it 2.76 r_scbond_other 2.76 r_mcangle_it 2.412 r_mcangle_other 2.412 r_angle_refined_deg 2.041 r_mcbond_it 1.664 r_mcbond_other 1.664 r_angle_other_deg 1.237 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.006 r_bond_other_d 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 7477 Nucleic Acid Atoms Solvent Atoms 1119 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing