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Crystal structure of truncated hemoglobin from Tetrahymena pyriformis, Fe(III) form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.0M ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.51 72.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.567 α = 90 b = 69.567 β = 90 c = 354.311 γ = 120
Symmetry Space Group P 65 2 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 ADSC QUANTUM 315r 2007-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 93.7 39669 37170 -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) 1.93 1.96 98.6 0.368 2 7.3
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 (All) 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 3AQ5 1.93 34.62 37507 35208 1887 93.87 0.21163 0.21163 0.20963 0.2112 0.25107 0.2519 RANDOM 44.494
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] 0.16 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.483 r_dihedral_angle_3_deg 15.133 r_dihedral_angle_1_deg 6.158 r_dihedral_angle_4_deg 6.052 r_scangle_it 5.416 r_scbond_it 3.774 r_angle_refined_deg 2.596 r_mcangle_it 1.915 r_mcbond_it 1.191 r_chiral_restr 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.483 r_dihedral_angle_3_deg 15.133 r_dihedral_angle_1_deg 6.158 r_dihedral_angle_4_deg 6.052 r_scangle_it 5.416 r_scbond_it 3.774 r_angle_refined_deg 2.596 r_mcangle_it 1.915 r_mcbond_it 1.191 r_chiral_restr 0.206 r_bond_refined_d 0.033 r_gen_planes_refined 0.014 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1854 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 86
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling