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Structure of GTP-bound L129F mutant Rab7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 291 0.2 M sodium formate, 10mM trimethylamine hydrochloride, and 20% polyethylene glycol 3,350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.554 α = 71.24 b = 89.335 β = 85.97 c = 89.378 γ = 85.91
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0 NSLS X6A
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 2.8 20 98.7 0.1 7.7 2 24170 23869 2 2
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 2.8 2.871 98.2 0.417 1.7 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2.8 19.88 24300 23869 1277 98.7 0.23678 0.22036 0.2161 0.27265 0.2818 RANDOM 29.888
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] -2.02 0.35 0.09 0.75 -1.21 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.853 r_dihedral_angle_4_deg 20.412 r_dihedral_angle_3_deg 20.314 r_dihedral_angle_1_deg 6.636 r_scangle_it 2.423 r_scbond_it 1.466 r_mcangle_it 1.269 r_angle_refined_deg 1.175 r_mcbond_it 0.722 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.853 r_dihedral_angle_4_deg 20.412 r_dihedral_angle_3_deg 20.314 r_dihedral_angle_1_deg 6.636 r_scangle_it 2.423 r_scbond_it 1.466 r_mcangle_it 1.269 r_angle_refined_deg 1.175 r_mcbond_it 0.722 r_nbtor_refined 0.321 r_symmetry_hbond_refined 0.295 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.088 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 7044 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 165
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling