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The human protein kinase Pim1 in complex with its consensus peptide 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 277 0.1 M MSPG, 30% PEG1K, 0.5% DMSO, SITTING DROP, VAPOR DIFFUSION, 277 K
Crystal Properties Matthews coefficient Solvent content 3.7 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.1 α = 90 b = 98.1 β = 90 c = 80.04 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 RAXIS HTC MULTILAYER MIRRORS 2004-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.55 42.48 99 0.13 9.7 6.7 14259 2.5
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 2.55 2.65 97 0.51 2.7 4.1
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 2.55 24.5 13501 714 98.9 0.195 0.192 0.1999 0.248 0.2508 RANDOM 33.66
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] 1.37 0.69 1.37 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_dihedral_angle_4_deg 20.114 r_dihedral_angle_3_deg 15.567 r_dihedral_angle_1_deg 6.188 r_scangle_it 2.995 r_angle_refined_deg 1.974 r_scbond_it 1.791 r_mcangle_it 1.236 r_angle_other_deg 0.858 r_mcbond_it 0.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_dihedral_angle_4_deg 20.114 r_dihedral_angle_3_deg 15.567 r_dihedral_angle_1_deg 6.188 r_scangle_it 2.995 r_angle_refined_deg 1.974 r_scbond_it 1.791 r_mcangle_it 1.236 r_angle_other_deg 0.858 r_mcbond_it 0.729 r_symmetry_vdw_other 0.276 r_nbd_refined 0.221 r_nbtor_refined 0.189 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.117 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.091 r_nbtor_other 0.088 r_bond_refined_d 0.017 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 2264 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing