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Crystal structure of yeast PAPS reductase with PAP, a product complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 30% w/v PEG 6000, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.418 α = 90 b = 63.082 β = 90 c = 323.96 γ = 90
Symmetry Space Group P 21 21 21
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 Si(1,1,1) 2006-08-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-08-03 M MAD 3 1 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97944 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97879, 0.91838, 0.97931 SSRL BL9-2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2 2.05 107.833 96.5 0.073 0.073 7.2 4.3 64994 62580 1 30.9
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) Redundancy Number Unique Reflections (All) 1,2 2.05 2.1 78.2 0.373 0.373 1.6 3 3655
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.1 40 55322 2802 98.23 0.196 0.193 0.1956 0.246 0.1898 RANDOM 36.637
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] 3.29 -1.17 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.991 r_dihedral_angle_4_deg 22.089 r_dihedral_angle_3_deg 15.702 r_dihedral_angle_1_deg 5.529 r_scangle_it 1.606 r_angle_refined_deg 1.178 r_scbond_it 1.026 r_mcangle_it 0.643 r_mcbond_it 0.373 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.991 r_dihedral_angle_4_deg 22.089 r_dihedral_angle_3_deg 15.702 r_dihedral_angle_1_deg 5.529 r_scangle_it 1.606 r_angle_refined_deg 1.178 r_scbond_it 1.026 r_mcangle_it 0.643 r_mcbond_it 0.373 r_nbtor_refined 0.301 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8175 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling