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X-ray structure of a novel thermostable hemoglobin from the actinobacterium Thermobifida fusca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UX8 PDB ENTRY 1UX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 ACETATE BUFFER PH 5.8, NACL 2.5 M
Crystal Properties Matthews coefficient Solvent content 2.52 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.617 α = 90 b = 84.617 β = 90 c = 77.921 γ = 120
Symmetry Space Group P 64 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 2.47 50 96.7 0.05 17.3 8.7 6119
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 (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 1UX8 2.48 72.55 5783 316 97.5 0.223 0.218 0.2254 0.315 0.2047 RANDOM 55.28
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] 0.91 0.45 0.91 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.383 r_dihedral_angle_3_deg 21.721 r_dihedral_angle_4_deg 19.83 r_dihedral_angle_1_deg 5.231 r_scangle_it 3.107 r_scbond_it 2.071 r_angle_refined_deg 1.551 r_mcangle_it 1.396 r_mcbond_it 0.822 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.383 r_dihedral_angle_3_deg 21.721 r_dihedral_angle_4_deg 19.83 r_dihedral_angle_1_deg 5.231 r_scangle_it 3.107 r_scbond_it 2.071 r_angle_refined_deg 1.551 r_mcangle_it 1.396 r_mcbond_it 0.822 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.308 r_nbd_refined 0.258 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1032 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing