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Non-antibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A3D PDB ENTRY 1A3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 26% PEG 4000, 0.24M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.8 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.712 α = 90 b = 68.712 β = 90 c = 68.712 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RIGAKU CCD MIRRORS 2008-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.65 34.4 100 0.09 10.6 10.8 13314 -3 23.9
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 1.65 1.71 99.9 0.53 2.1 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 1A3D 1.65 34.36 12547 638 99.3 0.191 0.189 0.2019 0.23 0.2306 RANDOM 28.78
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_3_deg 13.963 r_dihedral_angle_4_deg 12.062 r_dihedral_angle_1_deg 6.749 r_scangle_it 2.517 r_scbond_it 1.837 r_angle_refined_deg 1.459 r_mcangle_it 1.264 r_angle_other_deg 0.905 r_mcbond_it 0.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_3_deg 13.963 r_dihedral_angle_4_deg 12.062 r_dihedral_angle_1_deg 6.749 r_scangle_it 2.517 r_scbond_it 1.837 r_angle_refined_deg 1.459 r_mcangle_it 1.264 r_angle_other_deg 0.905 r_mcbond_it 0.806 r_symmetry_vdw_refined 0.298 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.257 r_mcbond_other 0.243 r_symmetry_vdw_other 0.205 r_nbtor_refined 0.194 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.092 r_nbtor_other 0.09 r_metal_ion_refined 0.02 r_symmetry_metal_ion_refined 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_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 925 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling PHASER phasing