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The X-ray structure of the cyanobacteria Synechocystis hemoglobin "cyanoglobin" with cyanide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLY PDB entry 1dly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 1.5M sodium citrate, 0.2M ammonium citrate, 20% sucrose, 3% dioxane, 25mM sodium cyanide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.97 68.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.06 α = 90 b = 84.06 β = 90 c = 64.62 γ = 90
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 RIGAKU RAXIS IV 2002-10-01 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2002-10-02 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 ROTATING ANODE RIGAKU 1.5418
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 1,2 1.68 32.49 75.2 0.055 15.3 4.92 37950 3 3
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) 1,2 1.68 1.74 5 0.343 2.1 1.02 254
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1dly 1.68 32.5 3 3 37837 1053 80.46 0.19921 0.1927 0.19236 0.1906 0.19921 RANDOM 28.241
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] -0.38 -0.38 0.75
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.658 r_dihedral_angle_1_deg 5.294 r_scbond_it 3.442 r_mcangle_it 1.927 r_angle_refined_deg 1.809 r_mcbond_it 1.019 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.134
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.658 r_dihedral_angle_1_deg 5.294 r_scbond_it 3.442 r_mcangle_it 1.927 r_angle_refined_deg 1.809 r_mcbond_it 1.019 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.134 r_chiral_restr 0.121 r_bond_refined_d 0.023 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 969 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement CRYSTAL data reduction d*TREK data scaling CNS phasing