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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, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.45 64.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.584 α = 90 b = 96.584 β = 90 c = 98.065 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 MARMOSAIC 300 mm CCD 2008-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2 68.81 100 0.11 11.5 4.3 30381 30379 1 1 14.47
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 2 2.11 100 0.411 3.7 4.3 4394
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2 68.81 1 30379 28841 1536 99.99 0.149 0.1391 0.13812 0.1398 0.17632 0.1774 RANDOM 15.021
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] -0.52 -0.52 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 21.519 r_dihedral_angle_3_deg 13.57 r_dihedral_angle_1_deg 6.399 r_scangle_it 4.946 r_scbond_it 3.427 r_angle_refined_deg 2.1 r_mcangle_it 2.046 r_mcbond_it 1.334 r_chiral_restr 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 21.519 r_dihedral_angle_3_deg 13.57 r_dihedral_angle_1_deg 6.399 r_scangle_it 4.946 r_scbond_it 3.427 r_angle_refined_deg 2.1 r_mcangle_it 2.046 r_mcbond_it 1.334 r_chiral_restr 0.216 r_bond_refined_d 0.034 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 56
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling