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GppNHp-Bound Rab21 GTPase at 2.50 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 6.5 277 15% PEG 4000, 10% Glycerol, 200mM Na thiocyanate, 50mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.87 56.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.834 α = 90 b = 99.719 β = 90 c = 105.76 γ = 90
Symmetry Space Group I 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 Osmic mirror 2003-09-16 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 2.5 50 95.6 0.067 21.2 5 13852 55.7
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) 2.5 2.57 99.2 0.387 4.8 5 1169
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 2.5 16 13857 13121 679 95.4 0.25 0.21744 0.21354 0.29285 0.3042 RANDOM 41.242
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] -3.36 6.5 -3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.517 r_dihedral_angle_4_deg 22.495 r_dihedral_angle_3_deg 15.936 r_dihedral_angle_1_deg 6.42 r_scangle_it 1.908 r_angle_refined_deg 1.42 r_scbond_it 1.321 r_mcangle_it 1.004 r_mcbond_it 0.823 r_angle_other_deg 0.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.517 r_dihedral_angle_4_deg 22.495 r_dihedral_angle_3_deg 15.936 r_dihedral_angle_1_deg 6.42 r_scangle_it 1.908 r_angle_refined_deg 1.42 r_scbond_it 1.321 r_mcangle_it 1.004 r_mcbond_it 0.823 r_angle_other_deg 0.811 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.245 r_symmetry_vdw_other 0.241 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.204 r_nbd_other 0.195 r_nbtor_refined 0.183 r_metal_ion_refined 0.155 r_mcbond_other 0.105 r_nbtor_other 0.084 r_chiral_restr 0.076 r_xyhbond_nbd_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 2490 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing