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Crystal Structure of HasAp Capturing Manganese Tetraphenylporphyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 100mM CAPS/NaOH (pH10.5), 1.2M Sodium phosphate monobasic/0.8M pottasium phosphate dibasic, 0.2M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.802 α = 90 b = 84.802 β = 90 c = 84.485 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 RAYONIX MX225-HS 2018-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
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 1.5 48.9 99.6 0.068 0.071 0.018 1 24.4 14.5 95073
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 1.5 1.53 93 1.11 1.175 0.375 0.624 9.4
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 MOLECULAR REPLACEMENT THROUGHOUT 3ELL 1.5 20 90071 4921 99.42 0.1231 0.1209 0.1219 0.1648 0.1643 RANDOM 19.98
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] 0.23 0.23 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_4_deg 19.151 r_dihedral_angle_3_deg 10.928 r_dihedral_angle_1_deg 6.436 r_rigid_bond_restr 3.906 r_angle_refined_deg 1.934 r_angle_other_deg 1.649 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_4_deg 19.151 r_dihedral_angle_3_deg 10.928 r_dihedral_angle_1_deg 6.436 r_rigid_bond_restr 3.906 r_angle_refined_deg 1.934 r_angle_other_deg 1.649 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3972 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 291
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing