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Crystal Structure of the HasAp V37G Mutant 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 3.6 293 50mM Citric acid/NaOH (pH 3.6), 10% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.037 α = 90 b = 62.233 β = 90 c = 63.383 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 4M 2019-07-26 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 1.35 39.8 99.9 0.045 0.047 0.012 1 27.8 14.4 45004
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 1.35 1.37 100 2.189 2.268 0.591 0.743 14.3
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 1.35 39.8 42753 2192 99.82 0.1575 0.1558 0.1562 0.1922 0.1929 RANDOM 25.636
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] -1.52 2.22 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.113 r_dihedral_angle_4_deg 21.051 r_dihedral_angle_3_deg 11.488 r_dihedral_angle_1_deg 6.259 r_rigid_bond_restr 1.57 r_angle_other_deg 1.502 r_angle_refined_deg 1.433 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.113 r_dihedral_angle_4_deg 21.051 r_dihedral_angle_3_deg 11.488 r_dihedral_angle_1_deg 6.259 r_rigid_bond_restr 1.57 r_angle_other_deg 1.502 r_angle_refined_deg 1.433 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1326 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 55
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing