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RAB domain of human RASEF in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G16 pdb entry 1g16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 20% PEG-3350, 0.2M KF, vapor diffusion, sitting drop
Crystal Properties Matthews coefficient Solvent content 2.57 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.275 α = 90 b = 42.524 β = 98.91 c = 75.656 γ = 90
Symmetry Space Group P 1 21 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 2006-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 50 94.9 0.077 8.1 3.4 29262
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) 2 2.07 69.5 0.751 1.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 1g16 2.15 20 24513 1377 99.106 0.214 0.2111 0.2138 0.2602 0.2539 thin shells 27.035
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] -0.075 0.194 0.951 -0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_4_deg 13.877 r_dihedral_angle_1_deg 6.801 r_mcangle_it 3.723 r_scangle_it 3.354 r_mcbond_it 2.911 r_scbond_it 2.447 r_angle_refined_deg 1.423 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_4_deg 13.877 r_dihedral_angle_1_deg 6.801 r_mcangle_it 3.723 r_scangle_it 3.354 r_mcbond_it 2.911 r_scbond_it 2.447 r_angle_refined_deg 1.423 r_angle_other_deg 0.924 r_mcbond_other 0.647 r_symmetry_vdw_other 0.247 r_nbd_refined 0.211 r_nbd_other 0.184 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.121 r_symmetry_vdw_refined 0.12 r_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2430 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 59
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction