2A1F

Crystal Structure of Uridylate kinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310% PEG4K, 0.1M Bis-Tris pH6.5, 0.6M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.369α = 94.85
b = 79.889β = 96.68
c = 79.899γ = 96.88
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979APS31-ID

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
12.12096.40.0658.41.7105743105743-3
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)
12.12.1788.70.1662.881.39707

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2BNE2.120-3105743105589525896.510.2130.212960.210310.26327RANDOM24.372
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]
0.660.670.33-0.540.540.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.446
r_dihedral_angle_4_deg18.91
r_dihedral_angle_3_deg17.066
r_dihedral_angle_1_deg6.136
r_scangle_it2.984
r_scbond_it2.042
r_angle_refined_deg1.332
r_mcangle_it1.268
r_mcbond_it1.127
r_angle_other_deg0.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.446
r_dihedral_angle_4_deg18.91
r_dihedral_angle_3_deg17.066
r_dihedral_angle_1_deg6.136
r_scangle_it2.984
r_scbond_it2.042
r_angle_refined_deg1.332
r_mcangle_it1.268
r_mcbond_it1.127
r_angle_other_deg0.801
r_symmetry_vdw_other0.224
r_xyhbond_nbd_other0.196
r_nbd_refined0.194
r_symmetry_vdw_refined0.194
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.189
r_nbd_other0.18
r_nbtor_refined0.167
r_mcbond_other0.16
r_nbtor_other0.083
r_chiral_restr0.072
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10678
Nucleic Acid Atoms
Solvent Atoms889
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing