☰ Navigation Tabs
Crystal structure of Phosphoribosylamine--glycine ligase (TM1250) from Thermotoga maritima at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 18% PEG-8000, 0.1M sodium cacodylate pH 6.5, 0.2M calcium acetate hydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 7 277 20% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.21 2.44 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.745 α = 90 b = 78.443 β = 95.06 c = 85.018 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 CCD ADSC 2004-03-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD APS water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2004-02-20 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1 2 SYNCHROTRON APS BEAMLINE 19-BM 0.979127,0.979292,0.964063 APS 19-BM
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 2.3 37.4 85.6 0.054 12.1 2 31749 54.3
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 2.3 2.36 88.2 0.632 1.3 1.9 2434
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 2.3 37.26 29714 1560 84.01 0.21572 0.21315 0.2236 0.26383 0.2697 RANDOM 44.622
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] 0.3 -0.69 2.77 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.517 r_dihedral_angle_4_deg 19.757 r_dihedral_angle_3_deg 17.106 r_dihedral_angle_1_deg 7.293 r_scangle_it 7.017 r_scbond_it 5.184 r_mcangle_it 2.76 r_mcbond_it 1.937 r_angle_refined_deg 1.491 r_angle_other_deg 0.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.517 r_dihedral_angle_4_deg 19.757 r_dihedral_angle_3_deg 17.106 r_dihedral_angle_1_deg 7.293 r_scangle_it 7.017 r_scbond_it 5.184 r_mcangle_it 2.76 r_mcbond_it 1.937 r_angle_refined_deg 1.491 r_angle_other_deg 0.811 r_mcbond_other 0.479 r_symmetry_vdw_other 0.22 r_nbd_refined 0.207 r_nbd_other 0.183 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.143 r_nbtor_other 0.089 r_chiral_restr 0.083 r_xyhbond_nbd_other 0.057 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6065 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALA data scaling SOLVE phasing REFMAC refinement CCP4 data scaling