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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 5Z1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 1.6M almmonium sulfate, pH8.4
Crystal Properties Matthews coefficient Solvent content 2.68 54.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.409 α = 90 b = 87.409 β = 90 c = 148.791 γ = 90
Symmetry Space Group P 43 21 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 CCD RAYONIX MX300-HS 2016-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
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 1.5 30 96.8 0.064 27.5 4.7 89774
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 1.5 1.55 98.1 0.63 1.9 3.9
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 5Z1X 1.5 30 85148 4525 96.73 0.12699 0.12563 0.1255 0.15195 0.1511 RANDOM 20.353
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] 0.35 0.35 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.297 r_sphericity_free 21.606 r_dihedral_angle_4_deg 19.179 r_dihedral_angle_3_deg 10.901 r_sphericity_bonded 7.626 r_dihedral_angle_1_deg 6.52 r_long_range_B_refined 2.852 r_long_range_B_other 2.447 r_scangle_other 1.693 r_rigid_bond_restr 1.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.297 r_sphericity_free 21.606 r_dihedral_angle_4_deg 19.179 r_dihedral_angle_3_deg 10.901 r_sphericity_bonded 7.626 r_dihedral_angle_1_deg 6.52 r_long_range_B_refined 2.852 r_long_range_B_other 2.447 r_scangle_other 1.693 r_rigid_bond_restr 1.463 r_mcangle_other 1.41 r_mcangle_it 1.409 r_scbond_it 1.381 r_scbond_other 1.37 r_angle_refined_deg 1.338 r_mcbond_it 1.131 r_mcbond_other 1.122 r_angle_other_deg 0.903 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3739 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing