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Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Zn2+-bound form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 300 mM zinc acetate, and 50 mM sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.293 α = 73.25 b = 48.537 β = 68.61 c = 49.034 γ = 89.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2019-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 1.1200 AichiSR BL2S1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 43.42 90.1 0.112 0.997 11.2 7.9 40100
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 48.4 1.039 0.66 1.7 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.6 20 38053 2014 90.01 0.195 0.192 0.2009 0.245 0.2574 RANDOM 17.479
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] -0.21 0.96 -0.51 -2.03 1.38 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.033 r_dihedral_angle_4_deg 20.644 r_rigid_bond_restr 15.638 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_1_deg 7.617 r_scangle_other 6.397 r_long_range_B_refined 6.07 r_long_range_B_other 5.83 r_scbond_it 5.248 r_scbond_other 5.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.033 r_dihedral_angle_4_deg 20.644 r_rigid_bond_restr 15.638 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_1_deg 7.617 r_scangle_other 6.397 r_long_range_B_refined 6.07 r_long_range_B_other 5.83 r_scbond_it 5.248 r_scbond_other 5.248 r_mcangle_other 3.333 r_mcangle_it 3.332 r_mcbond_it 2.836 r_mcbond_other 2.833 r_angle_refined_deg 1.933 r_angle_other_deg 1.452 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2430 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing