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PAB0955 crystal structure : a GTPase in GTP 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 12% peg4000, 0.1M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 10mM EDTA, 0.65mM GTP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.05 40.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.71 α = 90 b = 60.71 β = 90 c = 116.84 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 ADSC QUANTUM 4 mirror 2004-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.4 20 98.5 0.075 0.075 20.76 11.6 10245 10088 48.9
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 2.46 98.2 0.4 0.4 7.03 12 696
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 2.4 15 10203 9975 994 98.76 0.24201 0.24201 0.236 0.2422 0.325 0.2554 RANDOM 48.9
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] 3.63 1.82 3.63 -5.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.065 r_dihedral_angle_3_deg 19.379 r_dihedral_angle_4_deg 14.792 r_dihedral_angle_1_deg 5.844 r_scangle_it 1.698 r_mcangle_it 1.653 r_angle_refined_deg 1.192 r_scbond_it 1.123 r_mcbond_it 0.938 r_symmetry_hbond_refined 0.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.065 r_dihedral_angle_3_deg 19.379 r_dihedral_angle_4_deg 14.792 r_dihedral_angle_1_deg 5.844 r_scangle_it 1.698 r_mcangle_it 1.653 r_angle_refined_deg 1.192 r_scbond_it 1.123 r_mcbond_it 0.938 r_symmetry_hbond_refined 0.628 r_nbtor_refined 0.333 r_xyhbond_nbd_refined 0.31 r_nbd_refined 0.263 r_symmetry_vdw_refined 0.257 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1999 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing