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Crystal structure of LRP6P3E3P4E4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IJQ PDB ENTRY 1IJQ
Crystallization Crystal Properties Matthews coefficient Solvent content 3.03 59.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.815 α = 90 b = 42.699 β = 97.49 c = 119.879 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 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.9 30 98 0.1 9.4 4.1 66493 2
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 1.9 1.95 88.4 0.56 2 3
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 1IJQ 1.9 29.09 63115 3378 97.85 0.18284 0.18135 0.1819 0.21098 0.2134 RANDOM 23.951
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] -0.2 0.07 0.38 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.859 r_dihedral_angle_4_deg 14.084 r_dihedral_angle_3_deg 11.406 r_scangle_it 6.483 r_dihedral_angle_1_deg 6.087 r_scbond_it 4.282 r_mcangle_it 3.149 r_mcbond_it 1.759 r_angle_refined_deg 1.099 r_angle_other_deg 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.859 r_dihedral_angle_4_deg 14.084 r_dihedral_angle_3_deg 11.406 r_scangle_it 6.483 r_dihedral_angle_1_deg 6.087 r_scbond_it 4.282 r_mcangle_it 3.149 r_mcbond_it 1.759 r_angle_refined_deg 1.099 r_angle_other_deg 0.928 r_mcbond_other 0.313 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4848 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing