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Crystal Structure of Laccase from Cerrena sp. RSD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 1.4M ammonium sulfate, pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.626 α = 90 b = 88.795 β = 90 c = 147.815 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 RAYONIX MX300HE 2013-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.38 30 98.6 0.042 44.2 4.3 228137
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 1.38 1.43 95 0.27 4.8 2.7
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 1GYC 1.38 25 216276 11402 98.64 0.12719 0.12602 0.1261 0.14948 0.1497 RANDOM 17.117
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] 0.41 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_sphericity_free 25.905 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 10.167 r_sphericity_bonded 6.534 r_dihedral_angle_1_deg 6.396 r_long_range_B_refined 2.96 r_long_range_B_other 2.96 r_angle_refined_deg 1.156 r_rigid_bond_restr 1.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_sphericity_free 25.905 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 10.167 r_sphericity_bonded 6.534 r_dihedral_angle_1_deg 6.396 r_long_range_B_refined 2.96 r_long_range_B_other 2.96 r_angle_refined_deg 1.156 r_rigid_bond_restr 1.055 r_scangle_other 0.976 r_mcangle_it 0.909 r_mcangle_other 0.909 r_scbond_it 0.856 r_scbond_other 0.856 r_angle_other_deg 0.709 r_mcbond_it 0.708 r_mcbond_other 0.708 r_chiral_restr 0.067 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 7488 Nucleic Acid Atoms Solvent Atoms 1596 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing