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Crystal structure of sperm whale myoglobin reconstituted with manganese porphycene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.8 M ammonium sulfate, 100 mM Tris-HCl buffer at pH 8.2, 4% acetone and 10% trehalose
Crystal Properties Matthews coefficient Solvent content 3.17 61.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.953 α = 90 b = 80.699 β = 90 c = 106.82 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 16M 2020-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.27 50 99.9 0.144 0.997 9 6.56 23450
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.34 1.994 0.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.27 46.53 22241 1157 99.9 0.205 0.203 0.2091 0.249 0.2547 RANDOM 51.83
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] 5.36 0.61 -5.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_3_deg 21.266 r_dihedral_angle_4_deg 20.597 r_long_range_B_refined 10.829 r_dihedral_angle_1_deg 5.813 r_scbond_it 5.75 r_mcangle_it 5.14 r_angle_refined_deg 4.161 r_mcbond_it 3.654 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_3_deg 21.266 r_dihedral_angle_4_deg 20.597 r_long_range_B_refined 10.829 r_dihedral_angle_1_deg 5.813 r_scbond_it 5.75 r_mcangle_it 5.14 r_angle_refined_deg 4.161 r_mcbond_it 3.654 r_chiral_restr 0.14 r_gen_planes_refined 0.015 r_bond_refined_d 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing Aimless data scaling