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STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AL4 PDB ENTRY 1AL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.5 25 %(W/V) PEG 3350, 0.2 M LISO4, 0.1 M BIS TRIS AT PH 5.5, LIPIDIC CUBIC PHASE OF 7.7 MAG (SN-1-O-(CIS-7)TETRADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO LIPID.
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.639 α = 90 b = 62.794 β = 100.02 c = 30.664 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 2008-08-05 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 1.08 30.2 94.9 0.1 15.8 6.3 46435 2 5.5
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 1.08 1.1 65 0.42 2.4 3.6
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 1AL4 1.08 30.2 44055 2380 94.95 0.13167 0.13041 0.147 0.15461 0.1533 RANDOM 12.7
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] 0.34 0.11 -0.65 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_sphericity_free 16.436 r_dihedral_angle_3_deg 9.794 r_sphericity_bonded 7.531 r_scangle_it 7.117 r_scbond_it 5.307 r_dihedral_angle_1_deg 4.732 r_mcangle_it 4.018 r_rigid_bond_restr 2.878 r_mcbond_it 2.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_sphericity_free 16.436 r_dihedral_angle_3_deg 9.794 r_sphericity_bonded 7.531 r_scangle_it 7.117 r_scbond_it 5.307 r_dihedral_angle_1_deg 4.732 r_mcangle_it 4.018 r_rigid_bond_restr 2.878 r_mcbond_it 2.828 r_angle_refined_deg 1.704 r_mcbond_other 1.368 r_angle_other_deg 0.813 r_chiral_restr 0.151 r_bond_refined_d 0.02 r_gen_planes_refined 0.014 r_bond_other_d 0.007 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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_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 3 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing