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Crystal structure of the Ig5-FN1 tandem of human NCAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HAZ PDB entry 2HAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.09 α = 90 b = 155.84 β = 90 c = 71.75 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2008-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.79 30 98.7 0.095 14.92 40353 1 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.79 1.9 96.3 0.585 6.11 6259
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 and ARP THROUGHOUT PDB entry 2HAZ 1.8 30 35851 35851 4060 98.69 0.18816 0.18816 0.18343 0.2185 0.23022 0.2568 RANDOM 23.848
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] 1.01 -0.24 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_3_deg 12.724 r_dihedral_angle_1_deg 6.684 r_scangle_it 3.98 r_scbond_it 2.639 r_angle_refined_deg 1.567 r_mcangle_it 1.53 r_mcbond_it 0.991 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_3_deg 12.724 r_dihedral_angle_1_deg 6.684 r_scangle_it 3.98 r_scbond_it 2.639 r_angle_refined_deg 1.567 r_mcangle_it 1.53 r_mcbond_it 0.991 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3018 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 5
Software Software Software Name Purpose XDS data scaling MOLREP phasing PHASER phasing ARP model building REFMAC refinement XDS data reduction XSCALE data scaling