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Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with DMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 1.6 M sodium potassium phosphate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.115 α = 90 b = 58.021 β = 109.65 c = 60.853 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M KB mirrors 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.36 48.14 99.8 0.084 0.035 0.999 14.9 6.7 71897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 99.1 0.695 0.293 0.862 3.1 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 FOURIER SYNTHESIS THROUGHOUT 5OXU 1.36 48.14 68364 3517 99.81 0.16016 0.15967 0.1678 0.16961 0.1789 RANDOM 12.6
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] -0.44 0.5 -0.65 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.951 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 12.593 r_dihedral_angle_1_deg 5.454 r_long_range_B_refined 3.812 r_long_range_B_other 3.532 r_angle_refined_deg 1.318 r_scangle_other 1.178 r_mcangle_it 1.029 r_mcangle_other 1.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.951 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 12.593 r_dihedral_angle_1_deg 5.454 r_long_range_B_refined 3.812 r_long_range_B_other 3.532 r_angle_refined_deg 1.318 r_scangle_other 1.178 r_mcangle_it 1.029 r_mcangle_other 1.029 r_angle_other_deg 0.968 r_scbond_it 0.682 r_scbond_other 0.682 r_mcbond_it 0.565 r_mcbond_other 0.565 r_chiral_restr 0.083 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2530 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing