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Crystal structure of laccases from Pycnoporus sanguineus, izoform I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5
2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.75 74.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.55 α = 90 b = 185.55 β = 90 c = 185.55 γ = 90
Symmetry Space Group P 43 3 2
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 6M 2014-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 50 100 0.129 1 27.7 25.8 28947
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 100 1.12 0.9 3.78 26.8
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 2XYB 2.75 46.39 27498 1449 99.96 0.16367 0.16131 0.1704 0.20736 0.2101 RANDOM 52.629
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.858 r_dihedral_angle_4_deg 15.769 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_1_deg 7.395 r_long_range_B_other 7.374 r_long_range_B_refined 7.373 r_scangle_other 6.674 r_scbond_it 4.491 r_scbond_other 4.468 r_mcangle_it 3.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.858 r_dihedral_angle_4_deg 15.769 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_1_deg 7.395 r_long_range_B_other 7.374 r_long_range_B_refined 7.373 r_scangle_other 6.674 r_scbond_it 4.491 r_scbond_other 4.468 r_mcangle_it 3.986 r_mcangle_other 3.986 r_mcbond_it 2.702 r_mcbond_other 2.701 r_angle_refined_deg 1.604 r_angle_other_deg 0.997 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 3814 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing