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Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to BI-D1870
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 22.5% PEG 3350; 20 MM MAGNESIUM, CHLORIDE, 0.1M CHC BUFFER pH 7.5, STABILIZED WITH 20% (V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.477 α = 90 b = 72.683 β = 90 c = 83.042 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2016-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45869 LNLS W01B-MX2
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 2 28.41 98.4 0.065 0.031 0.998 13.8 5.3 22504 35.63
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 2.05 97.9 0.693 0.32 0.891 2.8 5.5
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 2V62 2 28.41 22467 1100 98 0.184 0.182 0.1948 0.221 0.2248 RANDOM 42.57
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] 9.6375 -11.6452 2.0078
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.91 t_omega_torsion 3.36 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.91 t_omega_torsion 3.36 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 2391 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 28
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUSTER refinement 2016 data reduction