2PEZ

Crystal structrue of deletion mutant of APS-kinase domain of human PAPS-synthetase 1 in complex with cyclic PAPS and dADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PEYpdb entry 2PEY

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, 2mM dADP, 2mM PAPS, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.09α = 90
b = 59.4β = 90
c = 139.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-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
11.430880.0725.115.734.2730746471219.5
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)
1.41.48870.35230.24.33.1211674

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 2PEY1.42057725649387.890.196950.194330.21981RANDOM16.825
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]
1.02-0.16-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.554
r_dihedral_angle_4_deg14.493
r_dihedral_angle_3_deg12.651
r_dihedral_angle_1_deg5.351
r_scangle_it3.965
r_scbond_it2.644
r_angle_refined_deg1.937
r_mcangle_it1.65
r_mcbond_it1.131
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.554
r_dihedral_angle_4_deg14.493
r_dihedral_angle_3_deg12.651
r_dihedral_angle_1_deg5.351
r_scangle_it3.965
r_scbond_it2.644
r_angle_refined_deg1.937
r_mcangle_it1.65
r_mcbond_it1.131
r_nbtor_refined0.314
r_xyhbond_nbd_refined0.237
r_nbd_refined0.215
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.16
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2600
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms82

Software

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