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Crystal Structure of HasAp with Co-octaethylporphyrin
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 4.5 293 30% PEG 8000, 100mM sodium acetate/acetic acid (pH 4.5), 200mM lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.28 α = 90 b = 76.12 β = 90 c = 168.62 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 PILATUS3 6M 2021-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
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 1.35 45.26 100 0.111 0.113 0.999 15.59 28.721 131672 26.49
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 1.35 1.39 100 4.534 4.618 0.504 1.25 27.322
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 45.26 125044 6525 99.97 0.1388 0.1375 0.1375 0.1621 0.1622 RANDOM 23.63
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] 0.22 0.38 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.089 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_3_deg 10.047 r_dihedral_angle_1_deg 6.366 r_rigid_bond_restr 2.077 r_angle_other_deg 1.501 r_angle_refined_deg 1.423 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.089 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_3_deg 10.047 r_dihedral_angle_1_deg 6.366 r_rigid_bond_restr 2.077 r_angle_other_deg 1.501 r_angle_refined_deg 1.423 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3984 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 218
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction