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Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP and AMPPCP to 2.1 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMU PDB ENTRY 2BMU - WITHOUT LIGANDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2MM UMP. 2MM AMPPCP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.8 M 1,6-HEXANEDIOL, 5 MM COCL2, AND 0.1 M SODIUM ACETATE, PH 4.6. HANGING DROP VAPOR DIFFUSION TECHNIQUE
Crystal Properties Matthews coefficient Solvent content 2.44 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.174 α = 90 b = 126.438 β = 90 c = 134.991 γ = 90
Symmetry Space Group P 21 21 21
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 VERTICALLY FOCUSING CYLINDRICAL MIRROR 2004-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 91.29 99.9 0.1 6 6.7 86630 -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 2.21 99.9 0.5 1.4 6.9
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BMU - WITHOUT LIGANDS 2.1 25 82168 4353 100 0.216 0.215 0.2223 0.242 0.2284 RANDOM 28.37
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] 0.89 0.79 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_4_deg 22.743 r_dihedral_angle_3_deg 16.049 r_dihedral_angle_1_deg 5.963 r_scangle_it 2.852 r_scbond_it 1.949 r_angle_refined_deg 1.559 r_mcangle_it 1.445 r_mcbond_it 1.316 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_4_deg 22.743 r_dihedral_angle_3_deg 16.049 r_dihedral_angle_1_deg 5.963 r_scangle_it 2.852 r_scbond_it 1.949 r_angle_refined_deg 1.559 r_mcangle_it 1.445 r_mcbond_it 1.316 r_angle_other_deg 0.889 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.201 r_nbd_other 0.187 r_symmetry_vdw_other 0.181 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.176 r_symmetry_vdw_refined 0.124 r_nbtor_other 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10212 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 319
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing