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PAB0955 crystal structure : a GTPase in GTP-gamma-S 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 5.6 291 13% PEG 4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 0.65mM GTP-gamma-S, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.17 α = 90 b = 60.17 β = 90 c = 115.89 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 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 2.08 50 94.6 0.069 0.069 17.75 6.5 15141 15034 45
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 2.08 2.15 64.2 0.232 0.232 6.36 4.7 893
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 2.08 15 13196 12488 1587 83.18 0.21691 0.21691 0.20835 0.29463 0.2989 RANDOM 45.443
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] 1.8 0.9 1.8 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.069 r_dihedral_angle_3_deg 18.189 r_dihedral_angle_4_deg 17.661 r_dihedral_angle_1_deg 5.595 r_scangle_it 1.921 r_mcangle_it 1.809 r_scbond_it 1.429 r_angle_refined_deg 1.296 r_mcbond_it 1.084 r_symmetry_hbond_refined 0.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.069 r_dihedral_angle_3_deg 18.189 r_dihedral_angle_4_deg 17.661 r_dihedral_angle_1_deg 5.595 r_scangle_it 1.921 r_mcangle_it 1.809 r_scbond_it 1.429 r_angle_refined_deg 1.296 r_mcbond_it 1.084 r_symmetry_hbond_refined 0.411 r_symmetry_vdw_refined 0.36 r_nbtor_refined 0.331 r_xyhbond_nbd_refined 0.324 r_nbd_refined 0.261 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1981 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing