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Crystal structure of laccase from Myceliophthora thermophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 3 ul protein (66 mg/ml) + 2 ul reservoir solution (0.1 M HEPES pH 7.5, 34 % PEG 400, 0.22 M CaCl2, 0.05 M glycine)
Crystal Properties Matthews coefficient Solvent content 2.9 57.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.449 α = 90 b = 128.426 β = 90 c = 163.624 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS3 2M 2015-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.62 48.23 99.6 0.109 0.123 0.055 0.995 7.6 4.9 89938 19.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.68 99.6 0.866 0.971 0.431 0.688 1.6 5
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 2Q9O 1.62 48.23 85258 4497 99.4 0.1521 0.1502 0.1532 0.1886 0.1765 RANDOM 25.441
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] -3.4 2.65 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.514 r_sphericity_free 22.604 r_dihedral_angle_4_deg 20.48 r_sphericity_bonded 15.734 r_dihedral_angle_3_deg 12.287 r_dihedral_angle_1_deg 7.047 r_rigid_bond_restr 6.105 r_angle_refined_deg 2.085 r_angle_other_deg 1.073 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.514 r_sphericity_free 22.604 r_dihedral_angle_4_deg 20.48 r_sphericity_bonded 15.734 r_dihedral_angle_3_deg 12.287 r_dihedral_angle_1_deg 7.047 r_rigid_bond_restr 6.105 r_angle_refined_deg 2.085 r_angle_other_deg 1.073 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4325 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 284
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction