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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 3.44 64.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.338 α = 90 b = 96.338 β = 90 c = 98.943 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 1.7 48.17 99.9 0.083 12.9 4.2 49441 48216 1 1 14.748
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 1.7 1.79 99.7 0.495 3 4.2 7234
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 1.7 48.17 46936 46936 2505 99.81 0.151 0.14793 0.14651 0.1461 0.17378 0.174 RANDOM 15.445
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] -0.11 -0.11 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.565 r_dihedral_angle_4_deg 20.527 r_dihedral_angle_3_deg 12.811 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.516 r_scbond_it 3.641 r_angle_refined_deg 2.519 r_mcangle_it 2.392 r_mcbond_it 1.488 r_chiral_restr 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.565 r_dihedral_angle_4_deg 20.527 r_dihedral_angle_3_deg 12.811 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.516 r_scbond_it 3.641 r_angle_refined_deg 2.519 r_mcangle_it 2.392 r_mcbond_it 1.488 r_chiral_restr 0.239 r_bond_refined_d 0.035 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 50
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling