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Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUK PDB ENTRY 1NUK AND 1V3E experimental model PDB 1V3E PDB ENTRY 1NUK AND 1V3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 18% ISOPROPANOL, 18% PEG 3350 AND 0.1 M TRI-CITRATE BUFFER PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.236 α = 90 b = 95.834 β = 90 c = 97.909 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77.2 CCD ADSC CCD MIRRORS 2006-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.8 30 98.9 0.09 15 6.9 55159 -3
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 1.8 1.86 90.4 0.52 2.3 5.5
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 1NUK AND 1V3E 1.8 30 52300 2800 98.8 0.154 0.152 0.1611 0.198 0.2039 RANDOM 11.79
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] 0.14 0.02 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 13.405 r_dihedral_angle_1_deg 12.687 r_dihedral_angle_3_deg 12.266 r_scangle_it 7 r_scbond_it 5.178 r_mcangle_it 3.58 r_mcbond_it 3.2 r_angle_refined_deg 1.532 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 13.405 r_dihedral_angle_1_deg 12.687 r_dihedral_angle_3_deg 12.266 r_scangle_it 7 r_scbond_it 5.178 r_mcangle_it 3.58 r_mcbond_it 3.2 r_angle_refined_deg 1.532 r_angle_other_deg 0.939 r_symmetry_vdw_other 0.211 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.195 r_nbd_other 0.193 r_chiral_restr 0.192 r_nbd_refined 0.19 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.159 r_nbtor_other 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 4373 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing