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Crystal structure of adenylosuccinate synthetase, PurA, from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 PEG 8000, Ethylene Glycol, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.85 α = 90 b = 106.39 β = 96.32 c = 114.53 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU JUPITER 210 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 34.47 99.2 0.066 0.082 0.048 0.969 14 5.7 101788 8.754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 98.6 0.167 0.206 0.119 0.97 2.9 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1DJ3 2.1 34.47 96693 5094 99.04 0.18549 0.18332 0.1934 0.22636 0.2347 RANDOM 20.368
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.78 r_dihedral_angle_4_deg 15.193 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 6.513 r_long_range_B_refined 5.055 r_long_range_B_other 5.055 r_scangle_other 3.497 r_mcangle_it 2.709 r_mcangle_other 2.709 r_scbond_it 2.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.78 r_dihedral_angle_4_deg 15.193 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 6.513 r_long_range_B_refined 5.055 r_long_range_B_other 5.055 r_scangle_other 3.497 r_mcangle_it 2.709 r_mcangle_other 2.709 r_scbond_it 2.173 r_scbond_other 2.173 r_angle_refined_deg 1.864 r_mcbond_it 1.694 r_mcbond_other 1.694 r_angle_other_deg 1.075 r_chiral_restr 0.199 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12660 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling AMoRE phasing