☰ Navigation Tabs
Improved ligand discovery using micro-beam data collection at the edge of protein crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 1.6 M Sodium Citrate pH 11.2
0.3 M Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.41 α = 90 b = 38.99 β = 107.64 c = 57.11 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 EIGER X 9M 2017-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-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 1.4 54.42 99.83 0.999 19.07 6.756 36603
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 1.4 1.44 0.922
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 2JIC 1.4 54.42 36603 1918 99.83 0.12963 0.12872 0.1285 0.14698 0.1464 RANDOM 14.141
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] 0.46 -0.03 -0.28 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.891 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_3_deg 10.211 r_long_range_B_refined 9.063 r_dihedral_angle_1_deg 7.684 r_long_range_B_other 7.528 r_scangle_other 3.665 r_scbond_it 2.644 r_scbond_other 2.642 r_angle_refined_deg 2.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.891 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_3_deg 10.211 r_long_range_B_refined 9.063 r_dihedral_angle_1_deg 7.684 r_long_range_B_other 7.528 r_scangle_other 3.665 r_scbond_it 2.644 r_scbond_other 2.642 r_angle_refined_deg 2.312 r_mcangle_other 1.623 r_mcangle_it 1.606 r_mcbond_it 1.13 r_angle_other_deg 1.126 r_mcbond_other 1.08 r_chiral_restr 0.148 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d 0.003 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 1480 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing