1XNJ

APS complex of human PAPS synthetase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X6VPDB ENTRY 1X6V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62901 mM APS soaked for 1 hour, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.5α = 90
b = 82.5β = 105
c = 133γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.984094.50.08412.87.110801642.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.175.90.7092.114.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT WITH INITIAL MERCURY PHASESTHROUGHOUTPDB ENTRY 1X6V1.98129.11060311060315581970.1870.1840.239RANDOM34.47
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]
1.421.810.86-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.521
r_scangle_it3.983
r_mcangle_it3.717
r_angle_refined_deg2.61
r_scbond_it2.604
r_mcbond_it2.424
r_angle_other_deg1.35
r_symmetry_vdw_refined0.303
r_nbd_other0.281
r_symmetry_vdw_other0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.521
r_scangle_it3.983
r_mcangle_it3.717
r_angle_refined_deg2.61
r_scbond_it2.604
r_mcbond_it2.424
r_angle_other_deg1.35
r_symmetry_vdw_refined0.303
r_nbd_other0.281
r_symmetry_vdw_other0.259
r_nbd_refined0.257
r_xyhbond_nbd_refined0.233
r_symmetry_hbond_refined0.233
r_chiral_restr0.166
r_nbtor_other0.11
r_bond_refined_d0.036
r_gen_planes_other0.024
r_gen_planes_refined0.02
r_bond_other_d0.005
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9198
Nucleic Acid Atoms
Solvent Atoms667
Heterogen Atoms108

Software

Software
Software NamePurpose
X-GENdata scaling
XDSdata reduction
XFITdata reduction
REFMACrefinement
X-GENdata reduction
XDSdata scaling