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The crystal structure of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G8F PDB ENTRIES 1G8F, 1D6J experimental model PDB 1D6J PDB ENTRIES 1G8F, 1D6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 285 91 mM sodium Citrate, 270 mM ammonium acetate, 12% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.21 α = 90 b = 82.55 β = 105.1 c = 133.6 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2003-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.75 30 0.069 11 3.6 159267 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 88 0.58 2.1 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT WITH INITIAL MERCURY PHASES THROUGHOUT PDB ENTRIES 1G8F, 1D6J 1.75 129.1 165305 156571 8203 99.69 0.16789 0.1663 0.177 0.19811 0.2074 RANDOM 24.273
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] -0.41 0.24 1.4 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.913 r_scangle_it 4.932 r_scbond_it 3.07 r_mcangle_it 2.163 r_angle_refined_deg 1.805 r_angle_other_deg 1.48 r_mcbond_it 1.227 r_symmetry_vdw_other 0.299 r_symmetry_vdw_refined 0.272 r_nbd_other 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.913 r_scangle_it 4.932 r_scbond_it 3.07 r_mcangle_it 2.163 r_angle_refined_deg 1.805 r_angle_other_deg 1.48 r_mcbond_it 1.227 r_symmetry_vdw_other 0.299 r_symmetry_vdw_refined 0.272 r_nbd_other 0.26 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.227 r_symmetry_hbond_refined 0.224 r_chiral_restr 0.13 r_nbtor_other 0.088 r_bond_refined_d 0.021 r_gen_planes_other 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 9192 Nucleic Acid Atoms Solvent Atoms 1091 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement X-GEN data reduction XDS data scaling XFIT data reduction