3QFF

Crystal Structure of ADP complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q2OPDB entry 3Q2O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, 5mM DTT, 9% glycerol, 10% PEG6000, Hampton Research Silver Bullet Bio additive C3/27 and 3mM ADP, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.421α = 90
b = 82.089β = 90
c = 166.768γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-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
11.9697.10.09114.4355699-339.42
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)
11.962.0882.10.8161.98

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 3Q2O1.9619.9755669283297.160.20150.19890.2515RANDOM34.6697
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.811
r_dihedral_angle_3_deg14.506
r_dihedral_angle_4_deg9.74
r_dihedral_angle_1_deg5.538
r_scangle_it3.03
r_scbond_it1.765
r_mcangle_it1.259
r_angle_refined_deg1.182
r_mcbond_it0.669
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.811
r_dihedral_angle_3_deg14.506
r_dihedral_angle_4_deg9.74
r_dihedral_angle_1_deg5.538
r_scangle_it3.03
r_scbond_it1.765
r_mcangle_it1.259
r_angle_refined_deg1.182
r_mcbond_it0.669
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5876
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms54

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction