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Crystal structure of PIM1 in complex with ARC-1411
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 22% PEG3350, 0.1 M ammonium sulfate, 0.1 M tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.954 α = 90 b = 97.954 β = 90 c = 80.814 γ = 120
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 2013-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.96 48.98 100 0.064 0.071 0.029 0.999 13.4 5.6 31721
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 1.96 2.03 100 0.826 0.919 0.393 0.709 5.4
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 2j2i 1.96 48.98 30151 1533 99.98 0.1633 0.1616 0.1714 0.1947 0.1972 RANDOM 46.597
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] 0.48 0.24 0.48 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.477 r_dihedral_angle_4_deg 17.32 r_dihedral_angle_3_deg 12.64 r_dihedral_angle_1_deg 7.023 r_angle_refined_deg 1.433 r_angle_other_deg 1.322 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.477 r_dihedral_angle_4_deg 17.32 r_dihedral_angle_3_deg 12.64 r_dihedral_angle_1_deg 7.023 r_angle_refined_deg 1.433 r_angle_other_deg 1.322 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing