2J4J

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP and AMPPCP to 2.1 Angstrom resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6PROTEIN 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 coefficientSolvent content
2.4446.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.174α = 90
b = 126.438β = 90
c = 134.991γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHVERTICALLY FOCUSING CYLINDRICAL MIRROR2004-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.191.2999.90.166.786630-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2199.90.51.46.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BMU - WITHOUT LIGANDS2.1258216843531000.2160.2150.242RANDOM28.37
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]
0.890.79-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.747
r_dihedral_angle_4_deg22.743
r_dihedral_angle_3_deg16.049
r_dihedral_angle_1_deg5.963
r_scangle_it2.852
r_scbond_it1.949
r_angle_refined_deg1.559
r_mcangle_it1.445
r_mcbond_it1.316
r_angle_other_deg0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.747
r_dihedral_angle_4_deg22.743
r_dihedral_angle_3_deg16.049
r_dihedral_angle_1_deg5.963
r_scangle_it2.852
r_scbond_it1.949
r_angle_refined_deg1.559
r_mcangle_it1.445
r_mcbond_it1.316
r_angle_other_deg0.889
r_symmetry_hbond_refined0.223
r_nbd_refined0.201
r_nbd_other0.187
r_symmetry_vdw_other0.181
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.176
r_symmetry_vdw_refined0.124
r_nbtor_other0.085
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms10212
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms319

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing