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Crystal structure of the kinase domain of human 3'-phosphoadenosine 5'-phosphosulphate synthetase 2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 298 PEG3350 18%, 0.2M Ammonium Citrate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.914 α = 90 b = 131.892 β = 104.58 c = 70.562 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 IMAGE PLATE RIGAKU RAXIS IV 2005-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 2.5 50 98.3 0.12 13.14 3.5 31749 1 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) 2.5 2.59 100 0.344 4.88 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 THROUGHOUT 2.5 30 1 30052 1601 97.92 0.215 0.21159 0.2119 0.27835 0.2774 RANDOM 15.764
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] -0.23 0.22 -0.92 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_1_deg 6.086 r_scangle_it 3.207 r_scbond_it 1.998 r_angle_refined_deg 1.668 r_mcangle_it 1.219 r_mcbond_it 0.706 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_1_deg 6.086 r_scangle_it 3.207 r_scbond_it 1.998 r_angle_refined_deg 1.668 r_mcangle_it 1.219 r_mcbond_it 0.706 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 6128 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing