2OFX

crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OFW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.3298reservoir: 0.2-0.4mM ammonium dihydrogenphosphate protein solution: 6 mg/ml protein, 2 mM PAPS, 2 mM ADP, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9938.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.4α = 90
b = 63.32β = 114.38
c = 61.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2004-12-17MSINGLE 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
11.892097.50.0790.07118.835.62856027832
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)
1.892.0194.50.1650.1489.35.134298

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 REPLACEMENTTHROUGHOUT2OFW1.92027683276697.140.1920.1870.236RANDOM13.1
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]
-0.220.111.16-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.381
r_dihedral_angle_4_deg15.15
r_dihedral_angle_3_deg14.637
r_dihedral_angle_1_deg6.03
r_scangle_it2.967
r_scbond_it2.021
r_angle_refined_deg1.571
r_mcangle_it1.26
r_mcbond_it0.773
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.381
r_dihedral_angle_4_deg15.15
r_dihedral_angle_3_deg14.637
r_dihedral_angle_1_deg6.03
r_scangle_it2.967
r_scbond_it2.021
r_angle_refined_deg1.571
r_mcangle_it1.26
r_mcbond_it0.773
r_nbtor_refined0.31
r_symmetry_hbond_refined0.252
r_symmetry_vdw_refined0.236
r_nbd_refined0.21
r_xyhbond_nbd_refined0.178
r_chiral_restr0.092
r_metal_ion_refined0.045
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3173
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms176

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction