3R5H

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q20PDB ENTRY 3Q20

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, 5mM DTT, 11% glycerol, 10% PEG 6000, Hampton Research Addition Screen Condition 46, 10mM MgCl2; Crystal soaked for one minute with 10mM AIR, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3146.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.442α = 90
b = 82.785β = 90
c = 168.233γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-02-16MSINGLE 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
12.22098.80.05422.574131241312-335.399
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3394.90.1990.2188.65

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3Q202.219.764125741257208999.360.18210.18210.17870.2484RANDOM29.1989
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_deg40.906
r_dihedral_angle_3_deg14.663
r_dihedral_angle_4_deg13.713
r_dihedral_angle_1_deg5.844
r_scangle_it3.183
r_scbond_it1.844
r_mcangle_it1.353
r_angle_refined_deg1.314
r_mcbond_it0.721
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.906
r_dihedral_angle_3_deg14.663
r_dihedral_angle_4_deg13.713
r_dihedral_angle_1_deg5.844
r_scangle_it3.183
r_scbond_it1.844
r_mcangle_it1.353
r_angle_refined_deg1.314
r_mcbond_it0.721
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5925
Nucleic Acid Atoms
Solvent Atoms557
Heterogen Atoms94

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection