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Crystal structure of PIM1 in complex with ARC-3126
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 1 M ammonium phosphate dibasic, 0.1 M acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.804 α = 90 b = 94.804 β = 90 c = 80.399 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 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.97 47.4 100 0.12 0.15 0.066 0.995 9.4 5 29127
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 1.97 2.04 100 0.679 0.857 0.381 0.759 2 4.9
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 1.97 47.4 27419 1503 99.41 0.1811 0.1789 0.1872 0.2216 0.2218 RANDOM 28.624
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] 0.4 0.2 0.4 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.632 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 7.577 r_angle_refined_deg 1.454 r_angle_other_deg 1.297 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.632 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 7.577 r_angle_refined_deg 1.454 r_angle_other_deg 1.297 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2307 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 117
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing