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Crystal Structure of HasAp with Fe-5,15-Diazaporphyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 50mM MES (pH6.0), 50mM KPi buffer (pH7.0), 500mM Potassium sodium tartrate
Crystal Properties Matthews coefficient Solvent content 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.002 α = 90 b = 154.002 β = 90 c = 36.626 γ = 120
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 MARMOSAIC 225 mm CCD 2015-09-28 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) 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 1.3 50 99.5 0.043 0.046 0.015 14.8 8.7 122191
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 1.3 1.35 96.9 0.303 0.332 0.133 0.926 5.8 11785
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 3W8O 1.3 19.05 115462 6109 99.06 0.169 0.1683 0.1681 0.1829 0.1829 RANDOM 15.876
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.441 r_dihedral_angle_4_deg 19.541 r_dihedral_angle_3_deg 9.728 r_dihedral_angle_1_deg 6.084 r_angle_refined_deg 1.618 r_angle_other_deg 0.885 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.441 r_dihedral_angle_4_deg 19.541 r_dihedral_angle_3_deg 9.728 r_dihedral_angle_1_deg 6.084 r_angle_refined_deg 1.618 r_angle_other_deg 0.885 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2670 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing