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Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z0I PDB ENTRY 1Z0I, 1TXU experimental model PDB 1TXU PDB ENTRY 1Z0I, 1TXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 10% PEG 6000, 0.2M MgCl2, 0.05 NaMES Microseeded, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.897 α = 90 b = 113.4 β = 90 c = 60.533 γ = 90
Symmetry Space Group P 21 21 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 Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.1 20 99.2 7.5 22 6 40412 -3
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) 2.1 2.154 38.5 4 1 40412
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 PDB ENTRY 1Z0I, 1TXU 2.1 20 28020 1500 99.91 0.19099 0.18821 0.1876 0.24272 0.2429 RANDOM 33.088
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] -1.17 -0.33 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.856 r_dihedral_angle_4_deg 19.829 r_dihedral_angle_3_deg 14.62 r_dihedral_angle_1_deg 5.24 r_scangle_it 3.211 r_scbond_it 1.994 r_mcangle_it 1.486 r_angle_refined_deg 1.23 r_mcbond_it 0.858 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.856 r_dihedral_angle_4_deg 19.829 r_dihedral_angle_3_deg 14.62 r_dihedral_angle_1_deg 5.24 r_scangle_it 3.211 r_scbond_it 1.994 r_mcangle_it 1.486 r_angle_refined_deg 1.23 r_mcbond_it 0.858 r_nbtor_refined 0.304 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.195 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.08 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_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3179 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing