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CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND PIMTIDE
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 = 97.889 α = 90 b = 97.889 β = 90 c = 80.493 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 2005-01-20 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 2.45 50 99.8 0.1 9.43 7.33 16216 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 2.45 2.55 99 0.55 3.28 6.24
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 2.45 42 15369 814 99.8 0.191 0.189 0.1965 0.225 0.2318 RANDOM 58.89
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] 2.43 1.21 2.43 -3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.334 r_dihedral_angle_4_deg 15.238 r_dihedral_angle_3_deg 14.729 r_dihedral_angle_1_deg 6.281 r_scangle_it 2.744 r_scbond_it 1.636 r_angle_refined_deg 1.451 r_mcangle_it 1.056 r_angle_other_deg 0.792 r_mcbond_it 0.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.334 r_dihedral_angle_4_deg 15.238 r_dihedral_angle_3_deg 14.729 r_dihedral_angle_1_deg 6.281 r_scangle_it 2.744 r_scbond_it 1.636 r_angle_refined_deg 1.451 r_mcangle_it 1.056 r_angle_other_deg 0.792 r_mcbond_it 0.593 r_symmetry_vdw_other 0.264 r_nbd_refined 0.207 r_nbtor_refined 0.184 r_nbd_other 0.178 r_symmetry_hbond_refined 0.171 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.084 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2223 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing