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GDP-Bound Rab23 GTPase crystallized in P2(1)2(1)2(1) space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Polyalanine Rab3a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 15% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 41.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.281 α = 90 b = 61.44 β = 89.99 c = 63.854 γ = 90
Symmetry Space Group P 21 21 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 2004-03-30 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 1.9 50 95.9 0.044 24.5 4 12482 12522 34.8
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) 1.9 1.96 79.4 0.268 5.3 4 834
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 1.9 8 12522 11684 600 96.21 0.243 0.2322 0.22982 0.2298 0.27761 0.2696 RANDOM 25.353
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] -0.76 1.44 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_4_deg 15.147 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 5.276 r_scangle_it 1.67 r_angle_refined_deg 1.085 r_scbond_it 0.996 r_mcangle_it 0.807 r_mcbond_it 0.462 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_4_deg 15.147 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 5.276 r_scangle_it 1.67 r_angle_refined_deg 1.085 r_scbond_it 0.996 r_mcangle_it 0.807 r_mcbond_it 0.462 r_nbtor_refined 0.294 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.062 r_bond_refined_d 0.009 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 1293 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing