☰ Navigation Tabs
Structure of the OpcA adhesion from Neisseria meningitidis determined by crystallization from the cubic mesophase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K24 PDB ENTRY 1K24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 18%(V/V) PEG400, 0.1 M POTASSIUM SULFATE, 0.05 M HEPES, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.86 α = 90 b = 42.5 β = 90 c = 150.3 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 CHESS F1
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 1.95 20 98.8 0.099 13.1 4.8 18131 2
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 1.95 2.06 99.8 0.49 2.7 4.7
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 ENTRY 1K24 1.95 10 17043 927 98.2 0.227 0.224 0.2252 0.272 0.2771 RANDOM 20.83
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] -0.11 0.71 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.545 r_dihedral_angle_4_deg 13.721 r_dihedral_angle_3_deg 13.391 r_scangle_it 12.061 r_scbond_it 9.647 r_dihedral_angle_1_deg 9.423 r_mcangle_it 6.208 r_mcbond_it 4.985 r_angle_refined_deg 1.15 r_symmetry_hbond_refined 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.545 r_dihedral_angle_4_deg 13.721 r_dihedral_angle_3_deg 13.391 r_scangle_it 12.061 r_scbond_it 9.647 r_dihedral_angle_1_deg 9.423 r_mcangle_it 6.208 r_mcbond_it 4.985 r_angle_refined_deg 1.15 r_symmetry_hbond_refined 0.44 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.228 r_chiral_restr 0.093 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 1767 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing