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Structure and ligand selection of hemoglobin II from Lucina pectinata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EBT PDB ENTRY 1EBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 7 298 Reactor: 0.2 mm inner diameter capillary with a three layer configuration (6 microL/ 3 microL/ 30 microL). Protein chamber: 30 mg/ml in 50 mM BIS-TRIS propane pH 7.0, 0.5 mM EDTA, agarose 0.08% (w/v). Precipitant chamber: Ammonium sulphate 2.0 M., Counter-diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.918 α = 90 b = 73.918 β = 90 c = 152.355 γ = 90
Symmetry Space Group P 42 21 2
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 MAR CCD 165 mm 2004-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.97749 ESRF BM16
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 1.93 20 99.6 0.05 28.81 10.5 32364 27.64
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 1.93 1.96 100 94 0.336 7 10.6 1587
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 (All) 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 1EBT 1.932 19.838 32318 1643 99.593 0.166 0.165 0.1665 0.1932 0.1908 RANDOM 30.42
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] 0.038 0.038 -0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_4_deg 20.129 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_1_deg 5.322 r_scangle_it 3.023 r_mcangle_it 2.641 r_scbond_it 2.343 r_mcbond_it 2.149 r_angle_refined_deg 1.841 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_4_deg 20.129 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_1_deg 5.322 r_scangle_it 3.023 r_mcangle_it 2.641 r_scbond_it 2.343 r_mcbond_it 2.149 r_angle_refined_deg 1.841 r_nbtor_refined 0.307 r_metal_ion_refined 0.276 r_symmetry_vdw_refined 0.264 r_chiral_restr 0.247 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.194 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2381 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement CNS refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction CNS phasing