☰ Navigation Tabs
STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A monovaccenin LIPID CUBIC PHASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XDC PDB ENTRY 2XDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8.5 1M LITHIUM SULFATE, 10 MM NICKEL CHLORIDE, 0.1 M TRIS HCL, PH 8.5, LIPIDIC CUBIC PHASE OF MONOVACCENIN (11.7 MAG)
Crystal Properties Matthews coefficient Solvent content 2.3 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.96 α = 90 b = 41.981 β = 107.25 c = 32.429 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 ADSC QUANTUM 315r TOROIDAL MIRROR 2009-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.7 22.9 96.9 0.05 23 4.7 6612 2 15.8
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 1.7 1.75 78.9 0.25 5 3.9
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 2XDC 1.7 22.88 6306 306 96.89 0.16823 0.16622 0.1662 0.21118 0.2133 RANDOM 17.281
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] 0.02 -0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.113 r_dihedral_angle_3_deg 13.357 r_dihedral_angle_1_deg 5.934 r_scangle_it 5.062 r_scbond_it 3.48 r_mcangle_it 2.6 r_angle_refined_deg 1.828 r_mcbond_it 1.646 r_chiral_restr 0.158 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.113 r_dihedral_angle_3_deg 13.357 r_dihedral_angle_1_deg 5.934 r_scangle_it 5.062 r_scbond_it 3.48 r_mcangle_it 2.6 r_angle_refined_deg 1.828 r_mcbond_it 1.646 r_chiral_restr 0.158 r_bond_refined_d 0.019 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 544 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing