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Crystal structure of Pim-1 kinase domain in complex with 2-methyl-5-phenylfuran-3-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XR1 PDB ENTRY 1XR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 1.0 M ammonium dihydrogen phosphate, 0.2 M sodium chloride, 0.1 M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.79 α = 90 b = 95.79 β = 90 c = 79.76 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 PSI PILATUS 6M 2006-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99190 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 25 99.4 0.116 9.1 3.7 21227 21108 -3 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.29 100 0.534 3.72 3.75
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 1XR1 2.2 23.95 21106 1056 99.52 0.16 0.1584 0.163 0.192 0.2017 RANDOM 38.94
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] -3.3463 -3.3463 6.6927
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.86 t_omega_torsion 3.02 t_angle_deg 0.97 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.86 t_omega_torsion 3.02 t_angle_deg 0.97 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2212 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 21
Software Software Software Name Purpose PHASER phasing BUSTER refinement XDS data reduction XSCALE data scaling