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Crystal structure of the synaptic protein neuroligin 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J06 PDB entry 1J06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 277 10% PEG-3000, 0.1M sodium phosphate-citrate, 0.3M sodium chloride, 0.01M calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.73 α = 90 b = 154.05 β = 90 c = 81.3 γ = 90
Symmetry Space Group P 21 21 2
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 210 2007-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.2 30 99.9 0.065 21.6 6.6 89603
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 2.2 2.25 0.47 4.5 6.6
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 1J06 2.2 29.68 85129 4474 99.93 0.16858 0.1669 0.1861 0.20075 0.2161 RANDOM 33.923
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] -0.38 0.21 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.652 r_dihedral_angle_4_deg 20.784 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_1_deg 6.169 r_scangle_it 2.837 r_scbond_it 1.906 r_angle_refined_deg 1.389 r_mcangle_it 1.268 r_angle_other_deg 0.865 r_mcbond_it 0.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.652 r_dihedral_angle_4_deg 20.784 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_1_deg 6.169 r_scangle_it 2.837 r_scbond_it 1.906 r_angle_refined_deg 1.389 r_mcangle_it 1.268 r_angle_other_deg 0.865 r_mcbond_it 0.758 r_symmetry_vdw_other 0.294 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.197 r_nbd_other 0.178 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.152 r_mcbond_other 0.149 r_chiral_restr 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8504 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing