☰ Navigation Tabs
Crystal structure of rat neurexin 1beta in the Ca2+ containing form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C4R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.44 49.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.683 α = 90 b = 195.719 β = 90 c = 103.867 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 103 CCD MARRESEARCH 2001-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97949 APS 19-BM
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 2.6 40.6 99.9 0.065 24.8 4.9 73949 73949 51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.8 0.423 0.423 4.3 4.7 3636
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 FOURIER SYNTHESIS THROUGHOUT 1C4R 2.6 20 73564 69823 3741 100 0.20482 0.20482 0.20273 0.2063 0.24401 0.2458 RANDOM 40.116
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] 2.91 -2.49 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.68 r_dihedral_angle_4_deg 18.155 r_dihedral_angle_3_deg 17.132 r_dihedral_angle_1_deg 7.43 r_scangle_it 2.778 r_scbond_it 1.729 r_angle_refined_deg 1.614 r_mcangle_it 1.143 r_mcbond_it 0.666 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.68 r_dihedral_angle_4_deg 18.155 r_dihedral_angle_3_deg 17.132 r_dihedral_angle_1_deg 7.43 r_scangle_it 2.778 r_scbond_it 1.729 r_angle_refined_deg 1.614 r_mcangle_it 1.143 r_mcbond_it 0.666 r_nbtor_refined 0.313 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.134 r_metal_ion_refined 0.113 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12101 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling