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Crystal Structure of Uridylate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BNE pdb entry 2BNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10% PEG4K, 0.1M Bis-Tris pH6.5, 0.6M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.99 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.369 α = 94.85 b = 79.889 β = 96.68 c = 79.899 γ = 96.88
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 MARRESEARCH 2003-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979 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 2.1 20 96.4 0.065 8.4 1.7 105743 105743 -3
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 2.17 88.7 0.166 2.88 1.3 9707
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2BNE 2.1 20 -3 105743 105589 5258 96.51 0.213 0.21296 0.21031 0.2161 0.26327 0.2654 RANDOM 24.372
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] 0.66 0.67 0.33 -0.54 0.54 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.446 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 17.066 r_dihedral_angle_1_deg 6.136 r_scangle_it 2.984 r_scbond_it 2.042 r_angle_refined_deg 1.332 r_mcangle_it 1.268 r_mcbond_it 1.127 r_angle_other_deg 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.446 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 17.066 r_dihedral_angle_1_deg 6.136 r_scangle_it 2.984 r_scbond_it 2.042 r_angle_refined_deg 1.332 r_mcangle_it 1.268 r_mcbond_it 1.127 r_angle_other_deg 0.801 r_symmetry_vdw_other 0.224 r_xyhbond_nbd_other 0.196 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.18 r_nbtor_refined 0.167 r_mcbond_other 0.16 r_nbtor_other 0.083 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10678 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing