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Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and TMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WPH PDB entry 1WPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M NH4 Citrate, 0.8 % w/v NDSB 256, 5 % w/v PEG 3350, 1 % v/v Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.136 α = 90 b = 136.136 β = 90 c = 55.418 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 ADSC QUANTUM 315 LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits 2006-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-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 2.1 50 100 0.081 8 5.1 22238 22238 -3 41.5
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 2.1 2.14 84 0.423 2.8 5.1
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 1WPH 2.1 40.39 21608 21608 1102 0.196 0.196 0.194 0.1986 0.247 0.2495 RANDOM 26.96
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] -0.28 -0.14 -0.28 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.212 r_dihedral_angle_4_deg 17.153 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.623 r_scangle_it 3.518 r_scbond_it 2.406 r_angle_refined_deg 1.842 r_mcangle_it 1.36 r_angle_other_deg 0.932 r_mcbond_it 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.212 r_dihedral_angle_4_deg 17.153 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.623 r_scangle_it 3.518 r_scbond_it 2.406 r_angle_refined_deg 1.842 r_mcangle_it 1.36 r_angle_other_deg 0.932 r_mcbond_it 0.926 r_symmetry_vdw_other 0.32 r_mcbond_other 0.276 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.206 r_nbtor_refined 0.189 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.102 r_nbtor_other 0.092 r_symmetry_hbond_refined 0.081 r_bond_refined_d 0.02 r_bond_other_d 0.009 r_gen_planes_refined 0.008 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 2741 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 51
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 MOLREP phasing