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Structure of an IgNAR-AMA1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z40 PDB ENTRIES 1Z40 and 1VER experimental model PDB 1VER PDB ENTRIES 1Z40 and 1VER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 0.1M phosphate citrate pH 4.2, 0.2M NaCl, 20% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.48 α = 90 b = 76.48 β = 90 c = 140.978 γ = 120
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 QUANTUM 4 mirrors 2006-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 0.96426 Photon Factory BL-18B
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 2.45 66.23 0.13 14.4 5 28622 28622 1 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 2.45 2.51 0.57 1.6 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1Z40 and 1VER 2.45 38.33 1 1 28622 28622 3222 93.94 0.19822 0.18877 0.1876 0.28183 0.2771 RANDOM 57.778
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] 2.15 1.08 2.15 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.045 r_dihedral_angle_3_deg 18.484 r_dihedral_angle_4_deg 15.331 r_dihedral_angle_1_deg 6.815 r_scangle_it 1.88 r_angle_refined_deg 1.34 r_scbond_it 1.217 r_mcangle_it 0.934 r_mcbond_it 0.538 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.045 r_dihedral_angle_3_deg 18.484 r_dihedral_angle_4_deg 15.331 r_dihedral_angle_1_deg 6.815 r_scangle_it 1.88 r_angle_refined_deg 1.34 r_scbond_it 1.217 r_mcangle_it 0.934 r_mcbond_it 0.538 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.099 r_bond_refined_d 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7198 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing