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PAB0955 crystal structure : a GTPase in GDP and PO4 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 5 277 8% PEG6000, 1M Lithium chloride, 50mM NaCl, 10% glycerol, 0.1M Citric Acid , 1mM GTP, 20mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.82 α = 90 b = 84.051 β = 90 c = 53.167 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH mirror 2004-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A
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 2.8 100 97.8 0.093 0.093 15.19 7.4 6880 6729 46.798
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 2.8 2.9 93.8 0.455 0.455 4.6 7.6 618
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YR6 2.8 15 6794 6680 663 98.11 0.232 0.232 0.225 0.346 0.2488 random 46.798
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] 1.29 -1.37 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.342 r_dihedral_angle_3_deg 21.117 r_dihedral_angle_4_deg 14.79 r_dihedral_angle_1_deg 5.736 r_mcangle_it 1.198 r_angle_refined_deg 1.175 r_scangle_it 1.092 r_scbond_it 0.716 r_mcbond_it 0.667 r_nbtor_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.342 r_dihedral_angle_3_deg 21.117 r_dihedral_angle_4_deg 14.79 r_dihedral_angle_1_deg 5.736 r_mcangle_it 1.198 r_angle_refined_deg 1.175 r_scangle_it 1.092 r_scbond_it 0.716 r_mcbond_it 0.667 r_nbtor_refined 0.347 r_symmetry_vdw_refined 0.295 r_nbd_refined 0.293 r_xyhbond_nbd_refined 0.282 r_symmetry_hbond_refined 0.197 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_refined 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 1999 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing