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The Crystal Structure of LIMK2a from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M HEPES ,7.3,10% w/vPEG 8000, 8%v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.86 57.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.223 α = 90 b = 104.175 β = 116.683 c = 96.443 γ = 90
Symmetry Space Group P 1 21 1
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 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 2.5 48.35 98.6 0.071 12.3 3.3 53195
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 2.5 2.58 0.721 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 48.35 53175 2728 98.443 0.212 0.2093 0.2093 0.2563 0.2536 59.277
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] -3.695 1.732 -3.07 3.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.973 r_dihedral_angle_4_deg 18.07 r_dihedral_angle_3_deg 14.654 r_lrange_other 8.066 r_lrange_it 8.062 r_dihedral_angle_1_deg 6.234 r_scangle_it 5.213 r_scangle_other 5.213 r_mcangle_it 5.054 r_mcangle_other 5.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.973 r_dihedral_angle_4_deg 18.07 r_dihedral_angle_3_deg 14.654 r_lrange_other 8.066 r_lrange_it 8.062 r_dihedral_angle_1_deg 6.234 r_scangle_it 5.213 r_scangle_other 5.213 r_mcangle_it 5.054 r_mcangle_other 5.054 r_scbond_it 3.121 r_scbond_other 3.121 r_mcbond_it 3.087 r_mcbond_other 3.087 r_angle_refined_deg 1.367 r_angle_other_deg 1.1 r_symmetry_nbd_refined 0.193 r_nbd_refined 0.191 r_nbd_other 0.17 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.071 r_ncsr_local_group_2 0.062 r_ncsr_local_group_3 0.061 r_ncsr_local_group_5 0.058 r_ncsr_local_group_4 0.057 r_ncsr_local_group_6 0.053 r_chiral_restr 0.05 r_ncsr_local_group_1 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8948 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing