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Crystal structure of Rabex-5delta and Rabaptin-5C21 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 2.0M NaH2PO4/K2HPO4, 0.05% n-octyl-beta-D-galactopyranoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.19 61.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.14 α = 90 b = 87.14 β = 90 c = 168.878 γ = 120
Symmetry Space Group P 31 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 2011-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 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 3.1 50 98.1 0.082 20.1 5.8 13730
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 3.1 3.21 100 0.643 2.4 6 13730
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 1TXU 3.1 50 12008 601 85.71 0.2666 0.264 0.2635 0.3153 0.3159 RANDOM 71.9543
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] -1.93 -0.97 -1.93 2.9
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 53.47 r_dihedral_angle_2_deg 38.473 r_dihedral_angle_3_deg 19.538 r_dihedral_angle_4_deg 12.566 r_dihedral_angle_1_deg 6 r_rigid_bond_restr 2.835 r_angle_refined_deg 1.268 r_chiral_restr 0.072 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3059 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling PHASER phasing