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GppNHp-Bound Rab21 GTPase at 2.05 A Resolution
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 8 277 18% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 54.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.357 α = 90 b = 36.567 β = 113.4 c = 86.666 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MAR scanner 300 mm plate Osmic mirror 2004-04-14 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 2.05 50 99.8 0.08 15.8 4 23946 35.1
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) 2.05 2.11 98.1 0.368 3.8 4 1952
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 Polyalanine Rab3a GTPase 2.05 12 24116 22613 1219 99.88 0.232 0.21425 0.21041 0.2208 0.28586 0.2903 RANDOM 23.139
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] -0.84 -0.9 0.66 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.772 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 13.691 r_dihedral_angle_1_deg 6.137 r_scangle_it 2.43 r_scbond_it 1.8 r_angle_refined_deg 1.26 r_mcbond_it 1.105 r_mcangle_it 1.028 r_angle_other_deg 0.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.772 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 13.691 r_dihedral_angle_1_deg 6.137 r_scangle_it 2.43 r_scbond_it 1.8 r_angle_refined_deg 1.26 r_mcbond_it 1.105 r_mcangle_it 1.028 r_angle_other_deg 0.755 r_xyhbond_nbd_refined 0.211 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.2 r_nbd_other 0.196 r_symmetry_vdw_other 0.18 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.154 r_mcbond_other 0.105 r_nbtor_other 0.082 r_chiral_restr 0.069 r_xyhbond_nbd_other 0.042 r_metal_ion_refined 0.042 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2395 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing