☰ Navigation Tabs
Crystal structure of the OcuKAI2d2 protein from Orobanche cumana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 6.5, 25% v/v PEG3350
Crystal Properties Matthews coefficient Solvent content 3.11 60.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.799 α = 90 b = 149.799 β = 90 c = 56.854 γ = 120
Symmetry Space Group P 64 2 2
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 EIGER X 16M 2018-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.987 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.19 49.08 91.38 0.75 24.02 20 19763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.27 71.8 0.38 0.85 15
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.19 49.08 18113 1812 91.37 0.2085 0.2233 0.2266 0.2336 RANDOM 40.861
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 0.22 0.43 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.132 r_dihedral_angle_1_deg 5.863 r_scangle_it 1.983 r_scangle_other 1.983 r_mcangle_it 1.884 r_mcangle_other 1.883 r_scbond_it 1.167 r_scbond_other 1.167 r_mcbond_it 1.116 r_mcbond_other 1.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.132 r_dihedral_angle_1_deg 5.863 r_scangle_it 1.983 r_scangle_other 1.983 r_mcangle_it 1.884 r_mcangle_other 1.883 r_scbond_it 1.167 r_scbond_other 1.167 r_mcbond_it 1.116 r_mcbond_other 1.116 r_angle_refined_deg 0.978 r_angle_other_deg 0.378 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.166 r_nbd_other 0.124 r_chiral_restr 0.047 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2073 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing