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crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with AMP(ATP), cadmium and sulfate ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H06 PDB ENTRY 2H06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.15 293 0.1M citric acid, 1.3M ammonium sulfate, 0.02M sodium dihydrogen phosphate, 0.4M sodium chloride, 0.01M ATP, 0.01M cadmium chloride, pH 4.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.236 α = 90 b = 170.236 β = 90 c = 61.82 γ = 120
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 2006-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 25 97.1 0.074 7.9 5.59 33914 32945
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 96.8 0.359 2.1 5.67 3289
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 (All) 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 PDB ENTRY 2H06 2.2 25 33914 32941 1672 97.13 0.208 0.205 0.205 0.2122 0.254 0.2584 RANDOM 36.369
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] 0.21 0.11 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_4_deg 17.364 r_dihedral_angle_3_deg 16.768 r_dihedral_angle_1_deg 5.393 r_rigid_bond_restr 2.956 r_sphericity_free 2.863 r_scangle_it 2.807 r_scbond_it 2.681 r_mcangle_it 1.628 r_sphericity_bonded 1.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_4_deg 17.364 r_dihedral_angle_3_deg 16.768 r_dihedral_angle_1_deg 5.393 r_rigid_bond_restr 2.956 r_sphericity_free 2.863 r_scangle_it 2.807 r_scbond_it 2.681 r_mcangle_it 1.628 r_sphericity_bonded 1.384 r_angle_refined_deg 1.163 r_mcbond_it 1.117 r_nbtor_refined 0.294 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 78
Software Software Software Name Purpose d*TREK data scaling CNS refinement REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction CNS phasing