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Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 150mM Dipotassium hydrogenphosphate, 17% PEG 3350, 150mM dimethyl(2-hydroxyethyl)ammonium propane sulfonate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5 75.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.581 α = 90 b = 117.422 β = 90 c = 123.332 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 315 2006-12-12 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-12-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97956, 0.97973 Photon Factory BL-5A
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 2.7 50 12.7 23619 23619 27.6
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) 2.7 2.75 0.288 2.07
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.7 48.08 23220 1121 98.2 0.273 0.273 0.2752 0.298 0.2976 RANDOM 77.7
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] -20.9 40.93 -20.02
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 5.91 c_mcangle_it 4.92 c_scbond_it 3.65 c_mcbond_it 2.83 c_angle_deg 1.5 c_improper_angle_d 0.75 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 5.91 c_mcangle_it 4.92 c_scbond_it 3.65 c_mcbond_it 2.83 c_angle_deg 1.5 c_improper_angle_d 0.75 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2899 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling SHARP phasing