2PEY

Crystal structure of deletion mutant of APS-kinase domain of human PAPS-synthetase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OFXPDB entry 2OFX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293reservoir: 16-20% PEG 3350, 0.25-0.15 M diammonium hydrogen citrate, drop: 3.2 mg/ml protein solution, 2mM dADP, 2mM APS, 5mM MgCl2, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.43α = 90
b = 59.75β = 90
c = 138.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDMARMOSAIC 225 mm CCD2006-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.8820970.0868.416.636.9300622920124.6
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)
1.88282.60.38838.74.145.43922

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 2OFX1.882026048291596.560.204140.198690.25344RANDOM20.686
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]
3.08-0.78-2.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.917
r_dihedral_angle_4_deg16.674
r_dihedral_angle_3_deg14.318
r_dihedral_angle_1_deg5.653
r_scangle_it3.327
r_scbond_it2.157
r_angle_refined_deg1.487
r_mcangle_it1.418
r_mcbond_it0.854
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.917
r_dihedral_angle_4_deg16.674
r_dihedral_angle_3_deg14.318
r_dihedral_angle_1_deg5.653
r_scangle_it3.327
r_scbond_it2.157
r_angle_refined_deg1.487
r_mcangle_it1.418
r_mcbond_it0.854
r_nbtor_refined0.307
r_nbd_refined0.201
r_symmetry_vdw_refined0.171
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.146
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2578
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
XDSdata reduction
MOLREPphasing