☰ Navigation Tabs
Crystal structure of the 5'-deoxynucleotidase YfbR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 10% w/v PEG 3350, 0.3 M NH4 CITRATE, 5 mM BETA-MERCAPTOETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.023 α = 90 b = 137.023 β = 90 c = 56.288 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 SBC-3 LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam-defining slits 2004-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 50 98.2 0.099 0.099 24.9 5 28633 28633 -3 39.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 87.8 0.58 0.58 1.4 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.1 28.41 22944 22944 1172 0.19 0.19 0.187 0.1937 0.237 0.24 RANDOM 26.58
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] -1.48 -0.74 -1.48 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.268 r_dihedral_angle_3_deg 15.664 r_dihedral_angle_4_deg 14.635 r_dihedral_angle_1_deg 6.57 r_scangle_it 4.322 r_scbond_it 3.08 r_angle_refined_deg 1.805 r_mcangle_it 1.624 r_mcbond_it 1.332 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.268 r_dihedral_angle_3_deg 15.664 r_dihedral_angle_4_deg 14.635 r_dihedral_angle_1_deg 6.57 r_scangle_it 4.322 r_scbond_it 3.08 r_angle_refined_deg 1.805 r_mcangle_it 1.624 r_mcbond_it 1.332 r_angle_other_deg 0.926 r_symmetry_vdw_refined 0.45 r_symmetry_vdw_other 0.343 r_mcbond_other 0.308 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.195 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.186 r_chiral_restr 0.105 r_nbtor_other 0.093 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing DM phasing MLPHARE phasing SHELXD phasing SHELXE model building O model building CCP4 phasing SOLVE phasing RESOLVE phasing ARP/wARP model building SHARP phasing autoSHARP phasing