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GppNHp-Bound Rab21 Q53G mutant GTPase
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 7 277 20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.2 α = 90 b = 77.425 β = 89.86 c = 107.965 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 2003-12-31 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 1.8 50 98.4 0.064 14.4 2 68656 26.5
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) 1.8 1.85 97.6 0.311 3.4 3 5610
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 1.8 8 68520 64433 3448 97.99 0.195 0.1902 0.18837 0.1877 0.22512 0.2237 RANDOM 19.077
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] 0.34 -0.59 -0.29 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.293 r_dihedral_angle_4_deg 21.362 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_1_deg 4.976 r_scangle_it 1.414 r_angle_refined_deg 1.026 r_scbond_it 0.887 r_mcangle_it 0.741 r_mcbond_it 0.414 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.293 r_dihedral_angle_4_deg 21.362 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_1_deg 4.976 r_scangle_it 1.414 r_angle_refined_deg 1.026 r_scbond_it 0.887 r_mcangle_it 0.741 r_mcbond_it 0.414 r_nbtor_refined 0.294 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.097 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.064 r_metal_ion_refined 0.056 r_bond_refined_d 0.006 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_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 4969 Nucleic Acid Atoms Solvent Atoms 1005 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing