☰ Navigation Tabs
PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 13% PEG4000, 20mM DTT, 10% glycerol, 50mM NaCl, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 0.65mM GDP, 1mM WO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.47 α = 90 b = 85.21 β = 94.61 c = 60.57 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 QUANTUM 4 mirror 2004-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 ESRF ID14-2
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 1.75 50 98.6 0.098 0.098 12.47 4.7 60611 59865 27.296
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) 1.75 1.8 93.5 0.372 0.372 5.91 4 4813
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 1YR6 1.75 15 60500 59763 6086 98.77 0.196 0.196 0.195 0.1961 0.247 0.2139 RANDOM 33.883
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] 0.23 0.78 -0.76 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.596 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 15.387 r_dihedral_angle_1_deg 4.918 r_scangle_it 2.198 r_mcangle_it 1.799 r_scbond_it 1.676 r_angle_refined_deg 1.215 r_mcbond_it 1.107 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.596 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 15.387 r_dihedral_angle_1_deg 4.918 r_scangle_it 2.198 r_mcangle_it 1.799 r_scbond_it 1.676 r_angle_refined_deg 1.215 r_mcbond_it 1.107 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.275 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.232 r_metal_ion_refined 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4216 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing