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crystal structure of the kinetoplastid kinetochore protein Trypanosoma brucei KKT3 Divergent Polo-Box domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other partial Se-Met model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 25% PEG3350, 0.1 M Bis-Tris pH 5.5 and 0.1 M tri-sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.998 α = 84.11 b = 52.485 β = 84.42 c = 102.152 γ = 73.25
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 PILATUS3 6M 2016-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.0072 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.92 50.68 99 0.155 0.184 0.098 0.976 5.1 3.4 19067 63.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.92 3 98.4 1.022 1.213 0.643 0.53 3.4
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 partial Se-Met model 2.92 50.68 18988 952 98.6 0.2515 0.2504 0.2539 0.2712 0.2658 RANDOM 81.54
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] 6.7368 -8.0496 -3.4721 1.8403 -23.9987 -8.577
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.98 t_omega_torsion 2.84 t_angle_deg 1.04 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.98 t_omega_torsion 2.84 t_angle_deg 1.04 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6169 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 14
Software Software Software Name Purpose DIALS data reduction Aimless data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction