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Crystal structure of Ig1 domain of mouse SynCAM 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z9M A MONOMER OF HUMAN SYNCAM 3 (NECTIN-LIKE MOLECULE 1) IG1, PROTEIN DATA BANK CODE 1Z9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 0.1 M HEPES, pH 6.5-7.0, 21% PEG5000 monomethyl ether, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.16 61.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.847 α = 75.91 b = 50.528 β = 77.02 c = 79.851 γ = 65.18
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 315 2008-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.21 50 93.9 0.092 15.27 3.6 27498 2.2 30.8
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) 2.21 2.26 64.1 0.4 3.39 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 A MONOMER OF HUMAN SYNCAM 3 (NECTIN-LIKE MOLECULE 1) IG1, PROTEIN DATA BANK CODE 1Z9M 2.21 50 2 29225 26095 1383 94 0.2 0.198 0.2165 0.245 0.2617 RANDOM 45.012
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] -1.96 -0.42 1.46 2.52 -3.35 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.183 r_dihedral_angle_4_deg 23.604 r_dihedral_angle_3_deg 18.302 r_dihedral_angle_1_deg 7.3 r_scangle_it 6.023 r_scbond_it 3.619 r_angle_refined_deg 2.234 r_mcangle_it 1.794 r_mcbond_it 0.971 r_chiral_restr 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.183 r_dihedral_angle_4_deg 23.604 r_dihedral_angle_3_deg 18.302 r_dihedral_angle_1_deg 7.3 r_scangle_it 6.023 r_scbond_it 3.619 r_angle_refined_deg 2.234 r_mcangle_it 1.794 r_mcbond_it 0.971 r_chiral_restr 0.161 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling