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Crystal structure of trout hemoglobin at 1.35 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUU PDB entry 1OUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 277 Protein solution (15 mg/mL CO-bound trout IV Hemoglobin, 0.025 M Sodium chloride, 0.010 M Tris-HCl pH 8.0) was mixed one to one with carbon monoxide flushed well solution to yield a final concentration of 22.5% PEG 1500 and 0.04-0.06 M MES/Acetate at pH 5.7. The solutions were pH-ed to verify that the crystallization conditions were at pH 5.7 due to the lower buffer molarity. Crystals were cryo-protected with 22.5% PEG 1500, 22.5% Ethylene glycol, 0.04-0.06 M MES/Acetate at pH 5.7 in a single step, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.455 α = 90 b = 63.162 β = 93.1 c = 78.702 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 MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97935 APS 23-ID-D
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 1.35 39.294 97.4 0.118 10.482 7 120196
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 1.35 1.38 77.8 0.459 2.306 4.2 6375
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 PDB entry 1OUU 1.35 39.294 120109 6037 97.384 0.172 0.17 0.1698 0.212 0.2145 RANDOM 20.16
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] -0.186 -0.778 -1.58 1.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_4_deg 14.171 r_dihedral_angle_1_deg 4.561 r_scangle_it 3.311 r_scbond_it 2.376 r_mcangle_it 1.459 r_angle_refined_deg 1.197 r_mcbond_it 1.11 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_4_deg 14.171 r_dihedral_angle_1_deg 4.561 r_scangle_it 3.311 r_scbond_it 2.376 r_mcangle_it 1.459 r_angle_refined_deg 1.197 r_mcbond_it 1.11 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4496 Nucleic Acid Atoms Solvent Atoms 817 Heterogen Atoms 188
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction