3Q2O

Crystal Structure of purK: N5-carboxyaminoimidazole ribonucleotide synthetase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K5Ihomology model of 3K5I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, 5mM DTT, 9% glycerol, 10% PEG6000, Hampton Research Silver Bullet Bio additive B5/17, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2846.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.43α = 90
b = 82.445β = 90
c = 166.621γ = 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
21x-ray100CCDADSC QUANTUM 3152010-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID
2SYNCHROTRONAPS BEAMLINE 24-ID-E0.9791APS24-ID-E

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
1,21.962096.90.10614.677.65624256242-3-334.171
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)
1,21.962.0781.30.752.74.97484

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUThomology model of 3K5I1.9619.965336453364284897.080.19730.19730.19520.2352RANDOM28.5343
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_deg41.207
r_dihedral_angle_3_deg13.967
r_dihedral_angle_4_deg12.728
r_dihedral_angle_1_deg5.341
r_scangle_it2.93
r_scbond_it1.686
r_mcangle_it1.233
r_angle_refined_deg1.109
r_mcbond_it0.655
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.207
r_dihedral_angle_3_deg13.967
r_dihedral_angle_4_deg12.728
r_dihedral_angle_1_deg5.341
r_scangle_it2.93
r_scbond_it1.686
r_mcangle_it1.233
r_angle_refined_deg1.109
r_mcbond_it0.655
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5876
Nucleic Acid Atoms
Solvent Atoms379
Heterogen Atoms2

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling