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Crystal structure of kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 290.15 1M NaH2PO4 and K2HPO4 (pH8.2)
Crystal Properties Matthews coefficient Solvent content 1.85 33.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43 α = 90 b = 76.52 β = 90 c = 148.47 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77.15 CCD ADSC QUANTUM 270 2015-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
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 1.85 30 99.6 11 5.8 628287
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3K2L 1.9 30 37563 1964 99.89 0.16833 0.16685 0.19642 0.2056 RANDOM 21.25
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] 1.48 -0.52 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 23.811 r_dihedral_angle_3_deg 14.926 r_long_range_B_refined 8.2 r_long_range_B_other 8.155 r_scangle_other 6.155 r_dihedral_angle_1_deg 4.9 r_scbond_it 4.021 r_scbond_other 4.021 r_mcangle_it 3.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 23.811 r_dihedral_angle_3_deg 14.926 r_long_range_B_refined 8.2 r_long_range_B_other 8.155 r_scangle_other 6.155 r_dihedral_angle_1_deg 4.9 r_scbond_it 4.021 r_scbond_other 4.021 r_mcangle_it 3.573 r_mcangle_other 3.573 r_mcbond_it 2.396 r_mcbond_other 2.395 r_angle_refined_deg 2.167 r_angle_other_deg 1.135 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3208 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data scaling MOLREP phasing