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Kringle domain of human Receptor Tyrosine Kinase-Like Orphan Receptor 1 (ROR1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BA5 6BA5,6OSN experimental model PDB 6OSN 6BA5,6OSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.8-1.2 M Sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.157 α = 90 b = 48.157 β = 90 c = 69.021 γ = 120
Symmetry Space Group P 32 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 EIGER X 4M 2018-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.4 41.71 99.8 0.101 0.063 0.985 18.3 7.4 18755 15.82
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 1.4 1.42 0.808 0.494 0.737 1.7
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 6BA5,6OSN 1.4 41.71 17717 1007 99.69 0.21127 0.21113 0.2587 0.21394 0.2537 RANDOM 18.007
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] 0.19 0.09 0.19 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.839 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 11.866 r_dihedral_angle_1_deg 6.845 r_rigid_bond_restr 4.839 r_scangle_other 4.512 r_scbond_it 4.286 r_scbond_other 4.276 r_long_range_B_other 4.074 r_long_range_B_refined 4.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.839 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 11.866 r_dihedral_angle_1_deg 6.845 r_rigid_bond_restr 4.839 r_scangle_other 4.512 r_scbond_it 4.286 r_scbond_other 4.276 r_long_range_B_other 4.074 r_long_range_B_refined 4.067 r_mcangle_it 3.335 r_mcangle_other 3.331 r_mcbond_it 3.096 r_mcbond_other 3.087 r_angle_refined_deg 2.158 r_angle_other_deg 1.644 r_chiral_restr 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 676 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing