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Crystal structure of N-terminal domain of Borealin (20-88) in complex with synthetic antibody fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QFA experimental model PDB 8T58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 292 0.1 M CAPS, 40 % v/v MPD
Crystal Properties Matthews coefficient Solvent content 3.42 64.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.432 α = 90 b = 72.432 β = 90 c = 243.129 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 9M mirrors 2024-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.84 34.06 100 0.059 0.999 9.7 11.9 65038
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.87 1.7 0.353
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 1.84 34.06 61029 3300 98.82 0.15748 0.15536 0.1673 0.19732 0.2056 RANDOM 46.586
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] -0.02 -0.01 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 17.315 r_dihedral_angle_3_deg 14.41 r_long_range_B_refined 7.794 r_scangle_other 7.785 r_long_range_B_other 7.76 r_dihedral_angle_1_deg 7.507 r_scbond_it 7.162 r_scbond_other 7.16 r_mcangle_it 5.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 17.315 r_dihedral_angle_3_deg 14.41 r_long_range_B_refined 7.794 r_scangle_other 7.785 r_long_range_B_other 7.76 r_dihedral_angle_1_deg 7.507 r_scbond_it 7.162 r_scbond_other 7.16 r_mcangle_it 5.522 r_mcangle_other 5.521 r_rigid_bond_restr 5.013 r_mcbond_other 4.717 r_mcbond_it 4.693 r_angle_refined_deg 1.625 r_angle_other_deg 1.448 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3803 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing