2G08

X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product-transition complex analog with Aluminum fluoride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BDUpdb entry 2BDU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 20 MINUTES IN WELL SOLUTION WITH 0.060 M magnesium chloride, 0.003 M aluminum chloride, 0.050 M sodium fluoride, 0.010 M uridine, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0159.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.044α = 90
b = 135.044β = 90
c = 39.049γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM-RMONTEL OPTICS2005-12-18SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.3567.5299.90.099119.0116.6933163
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)
12.352.41000.73631.946.082039

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2BDU2.3567.5233031167399.5630.1940.1940.19010.2603RANDOM43.413
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]
0.8580.4290.858-1.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.893
r_dihedral_angle_4_deg22.124
r_dihedral_angle_3_deg16.836
r_dihedral_angle_1_deg6.467
r_scangle_it2.875
r_scbond_it1.923
r_angle_refined_deg1.407
r_mcangle_it1.122
r_mcbond_it0.701
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.893
r_dihedral_angle_4_deg22.124
r_dihedral_angle_3_deg16.836
r_dihedral_angle_1_deg6.467
r_scangle_it2.875
r_scbond_it1.923
r_angle_refined_deg1.407
r_mcangle_it1.122
r_mcbond_it0.701
r_nbtor_refined0.304
r_nbd_refined0.205
r_xyhbond_nbd_refined0.18
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.121
r_chiral_restr0.104
r_metal_ion_refined0.056
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4652
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms10

Software

Software
Software NamePurpose
SAINTdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
MOLREPphasing