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Crystal Structure of Kinase Pim1 with P123M mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YWV APO Structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.8 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.315 α = 90 b = 99.315 β = 90 c = 80.561 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 CCD ADSC QUANTUM 4 2002-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 84.51 99.8 23005 1.5 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 APO Structure 2.2 84.51 1.5 23005 21771 1178 99.77 0.19724 0.19508 0.2059 0.23668 0.247 RANDOM 27.464
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] 1.49 0.74 1.49 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.941 r_scangle_it 2.584 r_scbond_it 1.531 r_angle_refined_deg 1.385 r_mcangle_it 1.089 r_angle_other_deg 0.906 r_mcbond_it 0.575 r_symmetry_vdw_other 0.297 r_nbd_other 0.237 r_nbd_refined 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.941 r_scangle_it 2.584 r_scbond_it 1.531 r_angle_refined_deg 1.385 r_mcangle_it 1.089 r_angle_other_deg 0.906 r_mcbond_it 0.575 r_symmetry_vdw_other 0.297 r_nbd_other 0.237 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.093 r_nbtor_other 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2231 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing