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Hemoglobin Glb2-1 of Lotus japonicus (cyano-ferric form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 28% PEG 4K, 200 mM ammonium citrate, 4% polypropylene glycol, and 100 mM KCN
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.928 α = 90 b = 127.656 β = 90 c = 152.733 γ = 90
Symmetry Space Group C 2 2 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 2021-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979263 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 152.73 100 0.05 15.2 5.8 47061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 0.434 2.9
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 1.6 76.37 44575 2365 99.78 0.17978 0.17842 0.1903 0.20558 0.2191 RANDOM 27.244
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] 0.95 1.13 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.281 r_dihedral_angle_2_deg 10.006 r_long_range_B_refined 8.476 r_long_range_B_other 8.469 r_scangle_other 7.498 r_dihedral_angle_1_deg 5.466 r_scbond_it 4.766 r_scbond_other 4.741 r_mcangle_it 3.555 r_mcangle_other 3.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.281 r_dihedral_angle_2_deg 10.006 r_long_range_B_refined 8.476 r_long_range_B_other 8.469 r_scangle_other 7.498 r_dihedral_angle_1_deg 5.466 r_scbond_it 4.766 r_scbond_other 4.741 r_mcangle_it 3.555 r_mcangle_other 3.555 r_mcbond_other 2.544 r_mcbond_it 2.543 r_angle_refined_deg 1.926 r_angle_other_deg 0.657 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing