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Crystal structure of mouse nectin-2 extracellular fragment D1-D2, 2nd crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FMK PDB ENTRY 4FMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293.15 13% w/v PEG3350, 0.42 M sodium isothiocyanate, 0.1 M MES, pH 6.0, cryoprotectant: 15% 2R,3R-butane-di-ol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 4.19 70.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.022 α = 90 b = 117.022 β = 90 c = 158.467 γ = 120
Symmetry Space Group P 31 2 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 MAR CCD 165 mm 2011-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.9792 NSLS X4C
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 3.35 40 99.2 0.09 18.7 5.6 18438 18438 -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 3.35 3.47 99.4 0.54 4 5.7
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 (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 4FMK 3.35 20 18438 17484 942 99.26 0.24921 0.24693 0.2491 0.29333 0.2904 RANDOM 135.057
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] 8.28 4.14 8.28 -12.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.056 r_dihedral_angle_3_deg 22.548 r_dihedral_angle_4_deg 19.326 r_dihedral_angle_1_deg 8.104 r_angle_other_deg 1.994 r_angle_refined_deg 1.643 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.056 r_dihedral_angle_3_deg 22.548 r_dihedral_angle_4_deg 19.326 r_dihedral_angle_1_deg 8.104 r_angle_other_deg 1.994 r_angle_refined_deg 1.643 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5108 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 259
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling