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Crystal Structure of the HasAp L85A 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 8.5 293 100mM Tris-HCl (pH 8.5), 20% PEG 8000, 200mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.119 α = 90 b = 125.104 β = 99.45 c = 66.176 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 EIGER X 4M 2018-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
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 1.85 45.16 98.7 0.098 0.116 0.061 0.996 10.4 3.5 41904
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 1.85 1.89 99.2 0.783 0.917 0.474 0.663 3.7
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 1.85 20 39685 2155 98.5 0.1685 0.1666 0.1786 0.2044 0.2144 RANDOM 18.938
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] -0.57 0.14 1.05 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.268 r_dihedral_angle_3_deg 11.289 r_dihedral_angle_4_deg 8.828 r_dihedral_angle_1_deg 6.484 r_angle_other_deg 1.424 r_angle_refined_deg 1.389 r_chiral_restr 0.063 r_gen_planes_refined 0.01 r_bond_refined_d 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.268 r_dihedral_angle_3_deg 11.289 r_dihedral_angle_4_deg 8.828 r_dihedral_angle_1_deg 6.484 r_angle_other_deg 1.424 r_angle_refined_deg 1.389 r_chiral_restr 0.063 r_gen_planes_refined 0.01 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3972 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 159
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing