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Crystal structure determination of Shortfin Mako (Isurus oxyrinchus) hemoglobin at 1.9 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GCV PDB ENTRY 1gcv
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 35% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.259 α = 90 b = 61.099 β = 96.49 c = 72.207 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2009-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 25.89 99.2 0.0756 4.8 2.79 41106 37830 2.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 98.8 0.3745 1 2.78 3482
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1gcv 1.9 25.89 38919 37830 2007 99.25 0.20192 0.19865 0.211 0.26809 0.2189 RANDOM 36.491
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] 0.04 -0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.384 r_dihedral_angle_3_deg 16.06 r_dihedral_angle_4_deg 13.951 r_dihedral_angle_1_deg 5.66 r_scangle_it 3.781 r_scbond_it 2.844 r_mcangle_it 1.767 r_angle_refined_deg 1.719 r_mcbond_it 1.161 r_symmetry_vdw_refined 0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.384 r_dihedral_angle_3_deg 16.06 r_dihedral_angle_4_deg 13.951 r_dihedral_angle_1_deg 5.66 r_scangle_it 3.781 r_scbond_it 2.844 r_mcangle_it 1.767 r_angle_refined_deg 1.719 r_mcbond_it 1.161 r_symmetry_vdw_refined 0.351 r_nbtor_refined 0.308 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.21 r_symmetry_hbond_refined 0.193 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4206 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 172
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling