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GDP-Bound Rab23 GTPase crystallized in C222(1) space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Polyalanine Rab3a GTPase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 27% PEG 6000, 200mM Na Citrate, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.01 α = 90 b = 71.333 β = 90 c = 65.684 γ = 90
Symmetry Space Group C 2 2 21
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 MAR scanner 300 mm plate Osmic mirror 2004-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.06 50 99.9 0.097 16.4 5 10035 10052 28.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.06 2.12 99.9 0.306 4.3 5 828
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 Polyalanine Rab3a GTPase 2.06 6 10052 9122 463 99.94 0.209 0.19606 0.19404 0.2343 0.2134 RANDOM 20.757
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] -0.7 -0.84 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.462 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_4_deg 13.402 r_dihedral_angle_1_deg 5.921 r_scangle_it 1.649 r_angle_refined_deg 1.065 r_scbond_it 1.019 r_mcangle_it 0.815 r_mcbond_it 0.47 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.462 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_4_deg 13.402 r_dihedral_angle_1_deg 5.921 r_scangle_it 1.649 r_angle_refined_deg 1.065 r_scbond_it 1.019 r_mcangle_it 0.815 r_mcbond_it 0.47 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.066 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 1234 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing