4Q7F

1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QFKpdb entry 3QFK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2295Protein: 7.0 mg/mL, 0.5M Sodium chloride, Tris-HCl pH 7.2, 0.5 mM TCEP, 1 mM Adenosine; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M Sodium HEPES, 22% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7254.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.584α = 90
b = 86.452β = 116.86
c = 95.647γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2014-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9830980.1020.10216.75.14489644896-319
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0197.20.620.622.95.22238

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3QFK1.9829.364220942209223697.960.188460.18690.21788RANDOM31.592
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]
0.290.885.7-4.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.566
r_dihedral_angle_4_deg11.416
r_dihedral_angle_3_deg9.598
r_long_range_B_refined6.308
r_long_range_B_other6.143
r_dihedral_angle_1_deg3.116
r_scangle_other2.218
r_mcangle_it1.875
r_mcangle_other1.875
r_angle_refined_deg1.493
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.566
r_dihedral_angle_4_deg11.416
r_dihedral_angle_3_deg9.598
r_long_range_B_refined6.308
r_long_range_B_other6.143
r_dihedral_angle_1_deg3.116
r_scangle_other2.218
r_mcangle_it1.875
r_mcangle_other1.875
r_angle_refined_deg1.493
r_scbond_it1.423
r_scbond_other1.422
r_mcbond_it1.154
r_mcbond_other1.154
r_angle_other_deg0.746
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4092
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms20

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling