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The x-ray crystal structure of ferrous Synechocystis hemoglobin with a covalent linkage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTX pdb entry 1RTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 31% PEG MME 5000, 0.1 M MES, 0.2 M ammonium sulfate, 0.01 M cadmium chloride, 0.01 M sodium hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.662 α = 90 b = 46.503 β = 90 c = 62.621 γ = 90
Symmetry Space Group P 21 21 21
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 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 37.27 99.93 0.046 0.248 6.83 11443 11435
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 1.8 1.86 99 0.143 9.6 6.68
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 1RTX 1.8 37.27 11443 11435 598 99.93 0.1912 0.19117 0.18875 0.1969 0.2385 0.2482 RANDOM 18.3
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] -0.09 -0.73 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.345 r_scangle_it 4.181 r_scbond_it 2.71 r_mcangle_it 1.723 r_angle_refined_deg 1.596 r_angle_other_deg 0.958 r_mcbond_it 0.946 r_symmetry_vdw_refined 0.331 r_symmetry_vdw_other 0.285 r_xyhbond_nbd_refined 0.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.345 r_scangle_it 4.181 r_scbond_it 2.71 r_mcangle_it 1.723 r_angle_refined_deg 1.596 r_angle_other_deg 0.958 r_mcbond_it 0.946 r_symmetry_vdw_refined 0.331 r_symmetry_vdw_other 0.285 r_xyhbond_nbd_refined 0.267 r_nbd_refined 0.256 r_nbd_other 0.238 r_symmetry_hbond_refined 0.226 r_chiral_restr 0.1 r_nbtor_other 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.016 r_gen_planes_other 0.016 r_metal_ion_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 969 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing