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Type-2 Cu-depleted fungus laccase from Trametes hirsuta at low dose of ionization radiation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 Protein solution 44 mg/ml in 0.02M potassium phosphate, pH 6.0. Reservoir solution is 30% PEG 1500, 0.02M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.653 α = 90 b = 77.051 β = 90 c = 130.216 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 CCD MAR CCD 165 mm 2005-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 60 97.5 0.09 9.5 3.1 35771 26.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 75
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3fpx 2 60 33936 1786 97.56 0.16322 0.16123 0.20025 0.193 RANDOM 26.619
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] -0.75 0.9 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.64 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 11.401 r_dihedral_angle_1_deg 6.206 r_scangle_it 2.681 r_scbond_it 1.823 r_angle_refined_deg 1.355 r_mcangle_it 1.104 r_mcbond_it 0.628 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.64 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 11.401 r_dihedral_angle_1_deg 6.206 r_scangle_it 2.681 r_scbond_it 1.823 r_angle_refined_deg 1.355 r_mcangle_it 1.104 r_mcbond_it 0.628 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3795 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 170
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling