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Substrate and dioxygen binding to the endospore coat laccase CotA from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GSK PDB ENTRY 1GSK
Crystallization Crystal Properties Matthews coefficient Solvent content 3.53 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.14 α = 90 b = 102.14 β = 90 c = 136.85 γ = 120
Symmetry Space Group P 31 2 1
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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14 ESRF ID14
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 2.4 30.04 99.9 0.04 12.48 3 32860 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 PDB ENTRY 1GSK 2.4 30.06 31143 1663 99.87 0.17942 0.17768 0.1863 0.21058 0.2169 RANDOM 23.074
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] 0.19 0.19 0.19 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.086 r_dihedral_angle_4_deg 21.149 r_dihedral_angle_3_deg 15.085 r_dihedral_angle_1_deg 7.236 r_angle_refined_deg 1.994 r_angle_other_deg 0.861 r_chiral_restr 0.109 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.086 r_dihedral_angle_4_deg 21.149 r_dihedral_angle_3_deg 15.085 r_dihedral_angle_1_deg 7.236 r_angle_refined_deg 1.994 r_angle_other_deg 0.861 r_chiral_restr 0.109 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4045 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOLREP phasing