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GEF domain of DENND 1B in complex with Rab GTPase Rab35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 289 0.1 M Magnesium Formate, 19% PEG 3350, 0.1 M HEPES (pH 7.4), 4mM n-Nonyl-beta-D-glucoside, 289K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.33 47.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.588 α = 90 b = 56.563 β = 95.63 c = 175.305 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2011-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 25 94 3.3 70529 66297 -1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 99.3
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 (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 SAD THROUGHOUT 2.1 24.89 64040 59538 4502 100 0.22957 0.22957 0.22667 0.2368 0.26871 0.2764 RANDOM 41.795
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] 1.48 5.39 -2.15 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.321 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 15.325 r_dihedral_angle_1_deg 6.125 r_scangle_it 5.62 r_scbond_it 4.615 r_mcangle_it 3.312 r_mcbond_it 2.594 r_mcbond_other 1.689 r_angle_refined_deg 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.321 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 15.325 r_dihedral_angle_1_deg 6.125 r_scangle_it 5.62 r_scbond_it 4.615 r_mcangle_it 3.312 r_mcbond_it 2.594 r_mcbond_other 1.689 r_angle_refined_deg 1.62 r_angle_other_deg 1.099 r_chiral_restr 0.094 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8386 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose CBASS data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling