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Crystal structure of DUF305 fragment from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QF9 PDB entry 2QF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1M Bis-Tris pH 5.5, 3M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.69 α = 90 b = 49.69 β = 90 c = 71.191 γ = 90
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 MAR CCD 165 mm 2007-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97930 APS 31-ID
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 1.35 50 99.7 0.042 9.9 7.2 37848 37848
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) 1.35 1.4 100 0.655 7 3775
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2QF9 1.35 25.01 37810 37810 1914 99.71 0.156 0.156 0.154 0.1504 0.188 0.1847 RANDOM 23.942
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.091 r_sphericity_free 16.551 r_dihedral_angle_4_deg 14.184 r_dihedral_angle_3_deg 13.488 r_sphericity_bonded 10.143 r_scangle_it 7.508 r_scbond_it 5.354 r_mcangle_it 5.051 r_dihedral_angle_1_deg 4.174 r_mcbond_it 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.091 r_sphericity_free 16.551 r_dihedral_angle_4_deg 14.184 r_dihedral_angle_3_deg 13.488 r_sphericity_bonded 10.143 r_scangle_it 7.508 r_scbond_it 5.354 r_mcangle_it 5.051 r_dihedral_angle_1_deg 4.174 r_mcbond_it 4.08 r_rigid_bond_restr 3.908 r_angle_refined_deg 1.328 r_nbtor_refined 0.31 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1282 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing