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Complex of the neisserial PorA P1.4 epitope peptide and two Fab- fragments (antibody MN20B9.34)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CE1 PDB ENTRY 1CE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE/ACETIC ACID (PH 4.0) AND 25% W/V PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.666 α = 90 b = 63.833 β = 86.58 c = 124.701 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 CCD MARRESEARCH 2000-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 40 96 0.08 14.3 3.5 60806 1
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 2.02 92.1 0.39 3.1 3.4
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 1CE1 1.95 30 56219 3002 96.2 0.2 0.198 0.1986 0.238 0.2392 RANDOM 22.19
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] -0.76 -0.11 1.14 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.747 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.671 r_dihedral_angle_1_deg 6.753 r_scangle_it 2.708 r_scbond_it 1.898 r_angle_refined_deg 1.408 r_mcangle_it 1.242 r_mcbond_it 0.785 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.747 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.671 r_dihedral_angle_1_deg 6.753 r_scangle_it 2.708 r_scbond_it 1.898 r_angle_refined_deg 1.408 r_mcangle_it 1.242 r_mcbond_it 0.785 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 6757 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing