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Crystal structure of Rabex-5CC and Rabaptin-5C21 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.15M MgAc2, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.007 α = 90 b = 28.857 β = 102.24 c = 107.973 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 315r 2012-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 SSRF BL17U
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 2.2 50 97.7 0.06 21.2 3.4 13816
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 2.2 2.28 85.8 0.28 3.4 3 13816
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1X79 2.2 15.03 13815 691 97.23 0.195 0.1929 0.2345 0.2449 RANDOM 58.5336
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] -1.33 -1.54 5.18 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.895 r_sphericity_bonded 41.078 r_sphericity_free 34.993 r_dihedral_angle_3_deg 20.955 r_dihedral_angle_4_deg 19.014 r_rigid_bond_restr 4.755 r_dihedral_angle_1_deg 4.661 r_angle_refined_deg 1.374 r_angle_other_deg 1.202 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.895 r_sphericity_bonded 41.078 r_sphericity_free 34.993 r_dihedral_angle_3_deg 20.955 r_dihedral_angle_4_deg 19.014 r_rigid_bond_restr 4.755 r_dihedral_angle_1_deg 4.661 r_angle_refined_deg 1.374 r_angle_other_deg 1.202 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1627 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection