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CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XWS PDB ENTRY 1XWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 3.7 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.529 α = 90 b = 97.529 β = 90 c = 80.726 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 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2005-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 50 99.6 0.06 14.42 5.55 34487 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 97.8 0.33 3.25 3.69
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 PDB ENTRY 1XWS 1.9 40 32701 1751 99.7 0.159 0.157 0.1636 0.19 0.1959 RANDOM 51.2
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 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.947 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 12.026 r_scangle_it 6.05 r_dihedral_angle_1_deg 5.449 r_scbond_it 4.084 r_mcangle_it 2.933 r_mcbond_it 1.952 r_angle_refined_deg 1.279 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.947 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 12.026 r_scangle_it 6.05 r_dihedral_angle_1_deg 5.449 r_scbond_it 4.084 r_mcangle_it 2.933 r_mcbond_it 1.952 r_angle_refined_deg 1.279 r_angle_other_deg 0.827 r_symmetry_vdw_other 0.31 r_nbd_refined 0.213 r_nbd_other 0.183 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.087 r_nbtor_other 0.079 r_symmetry_vdw_refined 0.043 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2204 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing