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Structure of Rabenosyn (458-503), Rab4 binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AIK Polyalanine-gp41 (PDB ID; 1AIK.pdb)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 10% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal Properties Matthews coefficient Solvent content 2.37 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.366 α = 90 b = 42.236 β = 90 c = 43.059 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate osmic mirror 2003-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 50 94.1 0.07 19.5 3 7561 25
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) 1.5 1.54 80.7 0.221 5.8 3 531
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT Polyalanine-gp41
(PDB ID; 1AIK.pdb) 1.5 6 7679 7104 335 93.67 0.208 0.19556 0.19511 0.2022 0.20537 0.2126 RANDOM 14.817
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] -0.59 -0.44 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 49.426 r_dihedral_angle_4_deg 19.785 r_dihedral_angle_3_deg 10.23 r_dihedral_angle_1_deg 4.025 r_angle_refined_deg 0.94 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.324 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 49.426 r_dihedral_angle_4_deg 19.785 r_dihedral_angle_3_deg 10.23 r_dihedral_angle_1_deg 4.025 r_angle_refined_deg 0.94 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.324 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.164 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.088 r_nbtor_other 0.075 r_chiral_restr 0.051 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 361 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing