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Crystal structure of RidL(1-200) complexed with VPS29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris pH8.0, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.312 α = 101.73 b = 82.049 β = 104.26 c = 87.332 γ = 104.77
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 MAR CCD 130 mm 2016-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 0.9792 AichiSR BL2S1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 96.6 0.106 0.116 0.063 10.3 3.7 37098
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 96.7 0.891 0.534 0.716 3.7 1805
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.46 31.86 31351 1665 81.81 0.19131 0.18955 0.1929 0.22494 0.228 RANDOM 52.801
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] -13.88 0.3 -0.19 0.95 -2.29 12.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.43 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_4_deg 14.56 r_dihedral_angle_1_deg 5.774 r_long_range_B_refined 5.663 r_long_range_B_other 5.644 r_scangle_other 3.771 r_mcangle_it 3.117 r_mcangle_other 3.117 r_scbond_it 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.43 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_4_deg 14.56 r_dihedral_angle_1_deg 5.774 r_long_range_B_refined 5.663 r_long_range_B_other 5.644 r_scangle_other 3.771 r_mcangle_it 3.117 r_mcangle_other 3.117 r_scbond_it 2.38 r_scbond_other 2.378 r_mcbond_it 1.985 r_mcbond_other 1.983 r_angle_refined_deg 1.392 r_angle_other_deg 0.937 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other 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 6147 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing