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Crystal Structure of the HasAp V37G/K59Q Mutant Capturing Iron 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 3.6 293 50mM Citric acid/NaOH (pH 3.6), 10% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.7 α = 90 b = 58.34 β = 90 c = 65.32 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.700 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.12 43.51 100 0.07 0.071 0.999 24.82 39.483 72261 22.925
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.15 99.9 4.39 4.447 0.487 1.2 38.848
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 1.12 43.51 68537 3649 99.97 0.1437 0.1429 0.1429 0.1586 0.1592 RANDOM 21.938
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] -0.46 0.73 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 37.032 r_dihedral_angle_2_deg 31.472 r_dihedral_angle_3_deg 12.691 r_dihedral_angle_1_deg 6.421 r_rigid_bond_restr 2.38 r_angle_other_deg 1.637 r_angle_refined_deg 1.612 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 37.032 r_dihedral_angle_2_deg 31.472 r_dihedral_angle_3_deg 12.691 r_dihedral_angle_1_deg 6.421 r_rigid_bond_restr 2.38 r_angle_other_deg 1.637 r_angle_refined_deg 1.612 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1243 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 55
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing