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GppNHp-Bound Rab33 GTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Polyalanine Rab5c GTPase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 20% PEG 6000, 10% Glycerol, 1M Lithium Chlroride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.194 α = 90 b = 56.194 β = 90 c = 55.039 γ = 120
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 2003-02-25 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 96.7 0.057 29 5 17431 31.5
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 84.2 0.249 7.7 5 1240
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 Rab5c GTPase 1.81 8 17435 16353 879 97.52 0.207 0.19082 0.18946 0.2004 0.21794 0.2289 RANDOM 22.211
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] -0.43 -0.21 -0.43 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.74 r_dihedral_angle_4_deg 15.906 r_dihedral_angle_3_deg 12.23 r_dihedral_angle_1_deg 5.458 r_scangle_it 1.915 r_scbond_it 1.349 r_angle_refined_deg 1.275 r_mcangle_it 1.059 r_mcbond_it 0.965 r_angle_other_deg 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.74 r_dihedral_angle_4_deg 15.906 r_dihedral_angle_3_deg 12.23 r_dihedral_angle_1_deg 5.458 r_scangle_it 1.915 r_scbond_it 1.349 r_angle_refined_deg 1.275 r_mcangle_it 1.059 r_mcbond_it 0.965 r_angle_other_deg 0.826 r_symmetry_vdw_other 0.261 r_nbd_refined 0.205 r_nbd_other 0.182 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.129 r_mcbond_other 0.123 r_xyhbond_nbd_other 0.096 r_symmetry_vdw_refined 0.096 r_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined 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 1269 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing