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Crystal structure of tt0497 from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ACY PDB ENTRY 2ACY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 micro batch using TERA micro batch using TERA
Crystal Properties Matthews coefficient Solvent content 1.47 15.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.911 α = 90 b = 45.727 β = 90 c = 49.958 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 V 2003-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 1.09 33.73 63.7 18506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.09 1.13 5.1
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 2ACY 1.3 33.71 14207 1594 100 0.18958 0.18666 0.1878 0.21632 0.217 RANDOM 8.975
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] 0.13 -0.08 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.303 r_scangle_it 3.168 r_scbond_it 2.07 r_angle_refined_deg 1.858 r_mcangle_it 1.326 r_mcbond_it 0.796 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.303 r_scangle_it 3.168 r_scbond_it 2.07 r_angle_refined_deg 1.858 r_mcangle_it 1.326 r_mcbond_it 0.796 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.111 r_bond_refined_d 0.027 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 677 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing