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The crystal structures of several mutants of pleurotus eryngii versatile peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 1.4 M ammonium sulfate, 0.1 M sodium cacodilate and 2% 1,3-propanedio, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.46 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.271 α = 90 b = 96.271 β = 90 c = 98.907 γ = 90
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 QUANTUM 4r 2007-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 48.14 99.9 0.062 17.2 5 71919 71863 1 1
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 1.58 99.5 0.454 3.3 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2VKA 1.5 48.14 71863 68227 3635 99.92 0.158 0.15142 0.15014 0.1486 0.17618 0.1749 RANDOM 14.535
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.675 r_dihedral_angle_4_deg 20.163 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 5.898 r_scangle_it 4.734 r_scbond_it 3.188 r_angle_refined_deg 2.856 r_mcangle_it 2.33 r_mcbond_it 1.466 r_chiral_restr 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.675 r_dihedral_angle_4_deg 20.163 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 5.898 r_scangle_it 4.734 r_scbond_it 3.188 r_angle_refined_deg 2.856 r_mcangle_it 2.33 r_mcbond_it 1.466 r_chiral_restr 0.228 r_bond_refined_d 0.036 r_gen_planes_refined 0.017 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 62
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling