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In vitro Crystal Structure of PAK4 in complex with Inka peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298.15 Tris-HCl, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.62 α = 90 b = 65.62 β = 90 c = 184.15 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2014-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.06 32.81 100 0.074 21.2 12.8 25890
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 4FIE 2.06 32.81 24538 1262 99.92 0.20081 0.19856 0.2054 0.24343 0.2513 RANDOM 40.805
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.899 r_dihedral_angle_4_deg 16.301 r_dihedral_angle_3_deg 15.6 r_long_range_B_refined 8.126 r_long_range_B_other 8.091 r_scangle_other 6.512 r_dihedral_angle_1_deg 6.421 r_mcangle_it 4.832 r_mcangle_other 4.83 r_scbond_it 4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.899 r_dihedral_angle_4_deg 16.301 r_dihedral_angle_3_deg 15.6 r_long_range_B_refined 8.126 r_long_range_B_other 8.091 r_scangle_other 6.512 r_dihedral_angle_1_deg 6.421 r_mcangle_it 4.832 r_mcangle_other 4.83 r_scbond_it 4.53 r_scbond_other 4.528 r_mcbond_it 3.69 r_mcbond_other 3.674 r_angle_refined_deg 2.035 r_angle_other_deg 0.971 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2419 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling xia2 data processing