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Crystal structure of the Rab GTPase Sec4p mutant - S29V in complex with Sec2p and GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Crystals were grown by mixing protein complex with a reservoir solution containing 24% PEG 3350, 0.2 M Sodium Citrate in a 1:1 ratio and with the addition of 10mM GDP to the drop.
Crystal Properties Matthews coefficient Solvent content 5.34 76.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.9 α = 90 b = 119.28 β = 90 c = 122.86 γ = 90
Symmetry Space Group I 2 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 CCD ADSC QUANTUM 315r mirrors 2009-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.08090 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 85.44 99.8 0.084 13.4 7.9 19416
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.51 3.8 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2EQB 2.9 85.44 16492 879 89.47 0.25993 0.25802 0.2542 0.29527 0.2923 RANDOM 68.868
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] -0.33 0.65 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_4_deg 22.777 r_dihedral_angle_3_deg 22.267 r_dihedral_angle_1_deg 7.092 r_angle_refined_deg 1.613 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_4_deg 22.777 r_dihedral_angle_3_deg 22.267 r_dihedral_angle_1_deg 7.092 r_angle_refined_deg 1.613 r_chiral_restr 0.111 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_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2823 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing