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Crystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 2.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5Y PDB ENTRY 1O5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.9 pH 6.90
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.001 α = 90 b = 52.136 β = 97.64 c = 73.33 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 72.55 98.2 0.079 12 8172
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 98.9 0.652 3.1
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1O5Y 2.8 72.55 7762 349 98.2 0.21858 0.21571 0.2267 0.27555 0.2547 RANDOM 22.388
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] -3.52 -1.26 1.55 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.853 r_scangle_it 4.847 r_scbond_it 3.309 r_angle_refined_deg 1.635 r_mcangle_it 1.061 r_angle_other_deg 0.878 r_mcbond_it 0.441 r_symmetry_hbond_refined 0.323 r_symmetry_vdw_other 0.28 r_nbd_refined 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.853 r_scangle_it 4.847 r_scbond_it 3.309 r_angle_refined_deg 1.635 r_mcangle_it 1.061 r_angle_other_deg 0.878 r_mcbond_it 0.441 r_symmetry_hbond_refined 0.323 r_symmetry_vdw_other 0.28 r_nbd_refined 0.232 r_nbd_other 0.231 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.159 r_nbtor_other 0.088 r_chiral_restr 0.081 r_bond_refined_d 0.017 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2173 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling CCP4 model building REFMAC refinement HKL-2000 data reduction CCP4 phasing