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Structure of K-26-DCP in complex with the K-26 tripeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y79 PDB 1Y79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.2M MgCl2, 0.1M sodium cacodylate, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.58 α = 97.72 b = 66.94 β = 90.71 c = 102 γ = 117.37
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 DECTRIS PILATUS 6M 2014-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.75 33 89 0.099 0.982 5.6 1.9 128529
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 1.75 1.78 55.2 0.277 2.3 1.8
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 PDB 1Y79 1.75 33 122085 6436 89.18 0.18651 0.18509 0.21326 0.2382 RANDOM 16.319
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] -0.43 -0.16 0.03 0.3 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.484 r_dihedral_angle_4_deg 13.747 r_dihedral_angle_3_deg 12.537 r_dihedral_angle_1_deg 7.06 r_long_range_B_refined 4.307 r_long_range_B_other 4.025 r_scangle_other 2.314 r_mcangle_it 1.584 r_mcangle_other 1.584 r_angle_refined_deg 1.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.484 r_dihedral_angle_4_deg 13.747 r_dihedral_angle_3_deg 12.537 r_dihedral_angle_1_deg 7.06 r_long_range_B_refined 4.307 r_long_range_B_other 4.025 r_scangle_other 2.314 r_mcangle_it 1.584 r_mcangle_other 1.584 r_angle_refined_deg 1.445 r_scbond_it 1.423 r_scbond_other 1.423 r_angle_other_deg 0.983 r_mcbond_it 0.971 r_mcbond_other 0.971 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 10510 Nucleic Acid Atoms Solvent Atoms 1026 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing