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Crystal structure of truncated hemoglobin from Tetrahymena pyriformis, Fe(II)-O2 form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLW PDB ENTRY 1DLW
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 4.48 72.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.355 α = 90 b = 69.355 β = 90 c = 353.761 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 2007-10-13 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 1.78 33.27 98.3 49777 48931 -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) 1.78 1.81 92.7 0.199 4.5 7.7
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 PDB ENTRY 1DLW 1.78 33.27 47142 46313 2471 98.24 0.18775 0.18775 0.18662 0.1869 0.20927 0.2117 RANDOM 39.604
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] 0.06 0.03 0.06 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_3_deg 14.856 r_dihedral_angle_4_deg 5.713 r_dihedral_angle_1_deg 5.396 r_scangle_it 4.637 r_scbond_it 3.226 r_angle_refined_deg 2.528 r_mcangle_it 1.631 r_mcbond_it 1.049 r_chiral_restr 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_3_deg 14.856 r_dihedral_angle_4_deg 5.713 r_dihedral_angle_1_deg 5.396 r_scangle_it 4.637 r_scbond_it 3.226 r_angle_refined_deg 2.528 r_mcangle_it 1.631 r_mcbond_it 1.049 r_chiral_restr 0.21 r_bond_refined_d 0.032 r_gen_planes_refined 0.015 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 216 Heterogen Atoms 90
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling