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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-propanediol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.45 64.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.23 α = 90 b = 96.23 β = 90 c = 98.73 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 1.6 48.12 98.3 0.077 13.9 4.3 59138 57998 1 1 13.182
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 1.6 1.69 97.1 0.433 3.2 4.3 8340
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 1.6 48.12 1 59138 55052 2944 98.07 0.159 0.15392 0.15255 0.1513 0.17945 0.1748 RANDOM 15.316
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] -0.08 -0.08 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 21.163 r_dihedral_angle_3_deg 12.313 r_dihedral_angle_1_deg 6.666 r_scangle_it 4.784 r_scbond_it 3.171 r_angle_refined_deg 2.342 r_mcangle_it 2.124 r_mcbond_it 1.303 r_chiral_restr 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 21.163 r_dihedral_angle_3_deg 12.313 r_dihedral_angle_1_deg 6.666 r_scangle_it 4.784 r_scbond_it 3.171 r_angle_refined_deg 2.342 r_mcangle_it 2.124 r_mcbond_it 1.303 r_chiral_restr 0.187 r_bond_refined_d 0.03 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 62
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling