☰ Navigation Tabs
STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y5M PDB ENTRY 2Y5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 30 %(W/V) POLYETHYLENE GLYCOL (PEG) 8000, 0.2 M NH4SO4, LIPIDIC CUBIC PHASE OF 8.8 MAG (SN-1-O-(CIS-8)HEXADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO 8.8 MAG.
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.616 α = 90 b = 62.783 β = 100.02 c = 30.602 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH MX-300 SI(111) DOUBLE CRYSTAL 2009-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 1.26 30.15 96.4 0.06 22.6 7.1 28320 2 9.7
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 1.26 1.29 76.9 0.28 3.5 3.2
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 2Y5M 1.26 30.15 28320 1536 96.43 0.14917 0.14803 0.1414 0.16983 0.1644 RANDOM 11.441
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] -0.91 -0.5 1.77 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_sphericity_free 18.263 r_sphericity_bonded 12.4 r_dihedral_angle_3_deg 8.763 r_scangle_it 7.775 r_scbond_it 6.05 r_mcangle_it 4.55 r_dihedral_angle_1_deg 4.523 r_rigid_bond_restr 3.804 r_mcbond_it 3.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_sphericity_free 18.263 r_sphericity_bonded 12.4 r_dihedral_angle_3_deg 8.763 r_scangle_it 7.775 r_scbond_it 6.05 r_mcangle_it 4.55 r_dihedral_angle_1_deg 4.523 r_rigid_bond_restr 3.804 r_mcbond_it 3.133 r_angle_refined_deg 1.775 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.017 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 816 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing