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PAB0955 crystal structure : a GTPase in GDP 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 GDP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.19 α = 90 b = 84.95 β = 95.07 c = 60.2 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 IMAGE PLATE RIGAKU RAXIS IV mirror 2004-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.542
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 2.3 50 97.9 0.065 0.065 12.54 3.35 26447 25913 38
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) 2.3 2.38 96.3 0.348 0.348 3.59 3.3 2468
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 (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 2.3 15 26446 25808 2607 97.95 0.19016 0.19016 0.191 0.264 0.2048 random 34.923
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] -0.37 0.72 -0.3 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.466 r_dihedral_angle_4_deg 20.74 r_dihedral_angle_3_deg 18.103 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.301 r_mcangle_it 1.898 r_scbond_it 1.609 r_angle_refined_deg 1.294 r_mcbond_it 1.11 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.466 r_dihedral_angle_4_deg 20.74 r_dihedral_angle_3_deg 18.103 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.301 r_mcangle_it 1.898 r_scbond_it 1.609 r_angle_refined_deg 1.294 r_mcbond_it 1.11 r_nbtor_refined 0.33 r_symmetry_hbond_refined 0.306 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.235 r_symmetry_vdw_refined 0.227 r_chiral_restr 0.083 r_bond_refined_d 0.011 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 4232 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data scaling AMoRE phasing