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Crystal structure of horse heart myoglobin reconstituted with manganese porphycene in resting state at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Hanging drop containing 1.5 M ammonium sulfate, 5 mg/mL of protein, 50 mM Tris-HCl and 5 mM potassium phosphate at pH 8.5 was equilibrated with the reserver solution containing 3.0 M ammonium sulfate and 100 mM Tris-HCl buffer at pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.75 29.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.575 α = 90 b = 28.706 β = 106.15 c = 62.702 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 CCD RIGAKU SATURN A200 mirrors 2014-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1
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 1.5 50 99.6 0.073 0.078 0.029 11.1 7 19335
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 1.5 1.53 93.8 0.526 0.584 0.249 0.851 5
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 3WI8 1.5 30 17192 937 94.19 0.1704 0.1683 0.1677 0.2077 0.2074 RANDOM 15.996
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] 0.14 0.12 -0.04 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.833 r_dihedral_angle_4_deg 19.285 r_dihedral_angle_3_deg 13.916 r_dihedral_angle_1_deg 4.989 r_angle_refined_deg 2.947 r_angle_other_deg 1.065 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.833 r_dihedral_angle_4_deg 19.285 r_dihedral_angle_3_deg 13.916 r_dihedral_angle_1_deg 4.989 r_angle_refined_deg 2.947 r_angle_other_deg 1.065 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1185 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 58
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building REFMAC phasing