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GppNHp bound Rab11 GTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Polyalanine Rab5c
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 NaCl, Glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal Properties Matthews coefficient Solvent content 2.7 54.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.946 α = 90 b = 73.946 β = 90 c = 148.197 γ = 90
Symmetry Space Group I 4 2 2
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 2003-06-05 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 50 99.8 0.058 31.6 7 14293 34.1
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 2.06 99.8 0.252 7.6 7 1139
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 2 6 14295 12992 697 99.81 0.197 0.18006 0.17753 0.1923 0.22829 0.2381 RANDOM 22.315
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] -0.3 -0.3 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.01 r_dihedral_angle_4_deg 13.849 r_dihedral_angle_3_deg 11.381 r_dihedral_angle_1_deg 5.213 r_scangle_it 1.782 r_scbond_it 1.196 r_angle_refined_deg 1.067 r_angle_other_deg 0.723 r_mcangle_it 0.723 r_mcbond_it 0.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.01 r_dihedral_angle_4_deg 13.849 r_dihedral_angle_3_deg 11.381 r_dihedral_angle_1_deg 5.213 r_scangle_it 1.782 r_scbond_it 1.196 r_angle_refined_deg 1.067 r_angle_other_deg 0.723 r_mcangle_it 0.723 r_mcbond_it 0.686 r_symmetry_vdw_other 0.294 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.174 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.139 r_mcbond_other 0.081 r_nbtor_other 0.077 r_metal_ion_refined 0.062 r_chiral_restr 0.056 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_xyhbond_nbd_other 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 1309 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing