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Crystal structure of laccase from Pediococcus acidilactici Pa5930 (Tris-HCl pH 8.5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 30% PEG1000 and 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.797 α = 90 b = 94.294 β = 90 c = 97.564 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 100 PIXEL DECTRIS PILATUS3 S 6M 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97925 ALBA XALOC
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 2.5 94.29 100 0.148 0.16 0.058 0.995 7.9 7.3 17180
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 2.5 2.6 100 0.904 0.97 0.35 0.758 7.5
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 3ZDW 2.5 67.8 16257 865 99.94 0.2227 0.2201 0.2208 0.2679 0.2688 RANDOM 48.517
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] -4.31 -2.64 6.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_3_deg 16.964 r_dihedral_angle_4_deg 15.798 r_dihedral_angle_1_deg 7.175 r_angle_refined_deg 1.264 r_angle_other_deg 1.095 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_3_deg 16.964 r_dihedral_angle_4_deg 15.798 r_dihedral_angle_1_deg 7.175 r_angle_refined_deg 1.264 r_angle_other_deg 1.095 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3697 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction