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Crystal structure of TTHA0845 from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other This protein model solved by MAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 8.35mg/mL Protein, 2% PEG3350, 20mM Zn(OAc)2, 10mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.12 60.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.883 α = 90 b = 95.883 β = 90 c = 119.01 γ = 120
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 RIGAKU JUPITER 210 mirrors 2004-11-08 M SINGLE WAVELENGTH 2 1 x-ray CCD RIGAKU JUPITER 210 2004-11-08 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.28220, 1.28280, 1.26000 SPring-8 BL26B2
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 2.4 30 99.9 0.04 37.4 6.3 47780 61.252
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 2.4 2.49 100 0.304 6.6 6.4 4755
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 MAD, MOLECULAR REPLACEMENT THROUGHOUT This protein model solved by MAD 2.4 30 45287 45287 2415 99.75 0.25198 0.25198 0.24977 0.2414 0.29351 0.2836 RANDOM 52.23
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] 0.11 0.06 0.11 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_4_deg 20.368 r_dihedral_angle_3_deg 18.24 r_dihedral_angle_1_deg 6.773 r_scangle_it 2.665 r_scbond_it 1.64 r_angle_refined_deg 1.394 r_mcangle_it 1.33 r_mcbond_it 0.742 r_symmetry_vdw_refined 0.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_4_deg 20.368 r_dihedral_angle_3_deg 18.24 r_dihedral_angle_1_deg 6.773 r_scangle_it 2.665 r_scbond_it 1.64 r_angle_refined_deg 1.394 r_mcangle_it 1.33 r_mcbond_it 0.742 r_symmetry_vdw_refined 0.382 r_metal_ion_refined 0.345 r_nbtor_refined 0.304 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.095 r_symmetry_metal_ion_refined 0.06 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 6219 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing