1X6V

The crystal structure of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G8FPDB ENTRIES 1G8F, 1D6J
experimental modelPDB 1D6JPDB ENTRIES 1G8F, 1D6J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.628591 mM sodium Citrate, 270 mM ammonium acetate, 12% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.21α = 90
b = 82.55β = 105.1
c = 133.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.75300.069113.61592671
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)
11.751.85880.582.13.2

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 ENTRIES 1G8F, 1D6J1.75129.1165305156571820399.690.167890.16630.19811RANDOM24.273
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]
-0.410.241.4-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.913
r_scangle_it4.932
r_scbond_it3.07
r_mcangle_it2.163
r_angle_refined_deg1.805
r_angle_other_deg1.48
r_mcbond_it1.227
r_symmetry_vdw_other0.299
r_symmetry_vdw_refined0.272
r_nbd_other0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.913
r_scangle_it4.932
r_scbond_it3.07
r_mcangle_it2.163
r_angle_refined_deg1.805
r_angle_other_deg1.48
r_mcbond_it1.227
r_symmetry_vdw_other0.299
r_symmetry_vdw_refined0.272
r_nbd_other0.26
r_nbd_refined0.229
r_xyhbond_nbd_refined0.227
r_symmetry_hbond_refined0.224
r_chiral_restr0.13
r_nbtor_other0.088
r_bond_refined_d0.021
r_gen_planes_other0.014
r_gen_planes_refined0.012
r_bond_other_d0.002
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 Atoms9192
Nucleic Acid Atoms
Solvent Atoms1091
Heterogen Atoms29

Software

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