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Steccherinum murashkinskyi laccase at 0.95 resolution
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 8.5 293 0.1M Tris pH 8.5, 0.2 ammoniun sulphate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.51 α = 90 b = 83.27 β = 90 c = 111.04 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 2008-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.803 EMBL/DESY, HAMBURG X13
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 0.95 8 94.4 0.07 10.44 3.2 981844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 1 96.1 0.668 2 3.2
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 3FPX 0.95 8 301501 15916 98.53 0.12209 0.12117 0.1226 0.13941 0.1403 RANDOM 13.028
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] -0.03 -0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.732 r_sphericity_free 26.915 r_dihedral_angle_4_deg 22.26 r_dihedral_angle_3_deg 10.993 r_sphericity_bonded 9.682 r_dihedral_angle_1_deg 6.896 r_rigid_bond_restr 5.387 r_long_range_B_refined 3.44 r_long_range_B_other 2.855 r_scangle_other 2.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.732 r_sphericity_free 26.915 r_dihedral_angle_4_deg 22.26 r_dihedral_angle_3_deg 10.993 r_sphericity_bonded 9.682 r_dihedral_angle_1_deg 6.896 r_rigid_bond_restr 5.387 r_long_range_B_refined 3.44 r_long_range_B_other 2.855 r_scangle_other 2.295 r_scbond_it 1.913 r_angle_refined_deg 1.804 r_scbond_other 1.798 r_mcangle_it 1.55 r_mcangle_other 1.498 r_mcbond_it 1.144 r_mcbond_other 1.114 r_angle_other_deg 0.91 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3739 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing