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Crystal structure of TTHA1254 (wild type) from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG3350, Tris, NaCl, Ammonium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.721 α = 90 b = 61.721 β = 90 c = 74.707 γ = 120
Symmetry Space Group P 31 2 1
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++ 2005-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.7 50 18129
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 2D4O 1.7 50 17189 933 97.66 0.16958 0.1683 0.1833 0.19485 0.176 RANDOM 22.655
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] 0.78 0.39 0.78 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.074 r_scangle_it 4.329 r_scbond_it 2.543 r_mcangle_it 1.566 r_angle_refined_deg 1.428 r_angle_other_deg 0.822 r_mcbond_it 0.815 r_symmetry_vdw_other 0.396 r_nbd_other 0.254 r_nbd_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.074 r_scangle_it 4.329 r_scbond_it 2.543 r_mcangle_it 1.566 r_angle_refined_deg 1.428 r_angle_other_deg 0.822 r_mcbond_it 0.815 r_symmetry_vdw_other 0.396 r_nbd_other 0.254 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.09 r_nbtor_other 0.083 r_symmetry_vdw_refined 0.049 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 1011 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing