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PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi (after GTP hydrolysis)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 293 0.1M tri-Na citrate pH 5.6, 15% PEG 4000, 0.2M ammonium acetate, 20mM DTT, 0.65mM GTP, 8mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60
Crystal Properties Matthews coefficient Solvent content 2.19 38.7314
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.189 α = 90 b = 60.189 β = 90 c = 116.512 γ = 120
Symmetry Space Group P 32 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 MAR CCD 130 mm MIRROR 2004-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 100 99 0.067 19.55 9.3 9973
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 2.4 2.45 98.8 0.404 0.404 5.76 9.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1YRB 2.4 15 10300 9913 981 99.23 0.221 0.212 0.2238 0.324 0.2575 RANDOM 50.15
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] 2.39 1.19 2.39 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.452 r_dihedral_angle_4_deg 20.114 r_dihedral_angle_3_deg 18.699 r_dihedral_angle_1_deg 5.467 r_scangle_it 1.744 r_mcangle_it 1.685 r_scbond_it 1.22 r_angle_refined_deg 1.19 r_mcbond_it 0.96 r_symmetry_hbond_refined 0.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.452 r_dihedral_angle_4_deg 20.114 r_dihedral_angle_3_deg 18.699 r_dihedral_angle_1_deg 5.467 r_scangle_it 1.744 r_mcangle_it 1.685 r_scbond_it 1.22 r_angle_refined_deg 1.19 r_mcbond_it 0.96 r_symmetry_hbond_refined 0.377 r_symmetry_vdw_refined 0.333 r_nbtor_refined 0.332 r_xyhbond_nbd_refined 0.292 r_nbd_refined 0.27 r_chiral_restr 0.074 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_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 2001 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling AMoRE phasing