☰ Navigation Tabs
YopM-InlB: Hybrid leucine-rich repeat protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6T PDB ENTRIES 1H6T AND 1JL5 experimental model PDB 1JL5 PDB ENTRIES 1H6T AND 1JL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 HANGING DROP VAPOUR DIFFUSION AT 293 K WITH A DROP SIZE OF 2 UL CONSISTING OF EQUAL VOLUMES OF PROTEIN AT A CONCENTRATION OF 10 MG/ML AND RESERVOIR SOLUTION (0.1 M TRICINE, PH 9.0, 28% PEG 1000, 10% GLYCEROL, 0.25M KCL). CRYSTALS WERE CRYO-PROTECTED WITH RESERVOIR-SOLUTION ADDITIONALLY CONTAINING 15% GLYCEROL AND FLASH-FROZEN IN LIQUID NITROGEN
Crystal Properties Matthews coefficient Solvent content 1.91 35.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.21 α = 90 b = 30.68 β = 90.98 c = 135.39 γ = 90
Symmetry Space Group C 1 2 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.5 20 96.3 0.07 13.88 3.8 38095
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 1.5 1.54 82.4 0.82 1.8 3.28
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 PDB ENTRIES 1H6T AND 1JL5 1.5 20 36193 1901 96.24 0.17712 0.17495 0.1841 0.21874 0.2194 RANDOM 18.462
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] 1.35 -0.82 -0.95 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.664 r_dihedral_angle_4_deg 20.275 r_dihedral_angle_3_deg 14.636 r_dihedral_angle_1_deg 7.095 r_angle_refined_deg 2.218 r_angle_other_deg 1.13 r_chiral_restr 0.13 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.664 r_dihedral_angle_4_deg 20.275 r_dihedral_angle_3_deg 14.636 r_dihedral_angle_1_deg 7.095 r_angle_refined_deg 2.218 r_angle_other_deg 1.13 r_chiral_restr 0.13 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_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 2218 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing