☰ Navigation Tabs
Crystal structure of Adenylosuccinate synthetase (AMPSase) (purA) from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Internal tracking number 226144E11. JCSG screen condition E11:
14.4% PEG 8000
20% v/v glycerol
80 mM Cacodylate pH 6.5
160 mM Calcium acetate
ButhA.00888.a.A1 PW33408 at 32.28 mg/ml., vapor diffusion, sitting drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.88 α = 109.35 b = 74.59 β = 90.01 c = 112.66 γ = 103.19
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 SATURN 944+ 2011-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 1.95 50 96.1 0.079 14.14 5.1 129329 -3 23.361
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 1.95 2 90.8 0.442 3 3.77
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 3HID 1.95 50 129328 6527 96.17 0.203 0.201 0.2066 0.247 0.2537 RANDOM 19.263
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] -1.06 0.86 0.36 2.38 0.59 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.704 r_dihedral_angle_4_deg 16.049 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_1_deg 6.644 r_angle_refined_deg 1.441 r_angle_other_deg 0.89 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.704 r_dihedral_angle_4_deg 16.049 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_1_deg 6.644 r_angle_refined_deg 1.441 r_angle_other_deg 0.89 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12667 Nucleic Acid Atoms Solvent Atoms 1128 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction