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artificial dinuclear Mn-bound metalloprotein 2 (D2:Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Li2SO4, 20 % PEG 4000, pH 8.0 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.481 α = 90 b = 52.336 β = 114.01 c = 80.581 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 S 9M 2024-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979330 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.84 50 99.6 0.112 0.123 0.049 0.986 7.5 6 38116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.87 99 0.541 0.612 0.279 0.784 4.5
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 31.9 33331 1752 99.64 0.20054 0.19813 0.2053 0.24699 0.2543 RANDOM 21.738
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] -0.47 0.36 -0.43 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.352 r_dihedral_angle_1_deg 6.776 r_long_range_B_refined 6.53 r_long_range_B_other 6.443 r_dihedral_angle_2_deg 5.354 r_scangle_other 5.201 r_scbond_it 3.348 r_scbond_other 3.347 r_mcangle_other 2.702 r_mcangle_it 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.352 r_dihedral_angle_1_deg 6.776 r_long_range_B_refined 6.53 r_long_range_B_other 6.443 r_dihedral_angle_2_deg 5.354 r_scangle_other 5.201 r_scbond_it 3.348 r_scbond_other 3.347 r_mcangle_other 2.702 r_mcangle_it 2.701 r_mcbond_it 1.921 r_mcbond_other 1.917 r_angle_refined_deg 1.521 r_angle_other_deg 0.554 r_chiral_restr 0.076 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3022 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling XDS data reduction MOLREP phasing