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Crystal structure of the Lsd19-lasalocid A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGA PDB ENTRY 3RGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291.15 1.65 M sodium formate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 3.99 69.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.14 α = 90 b = 140.14 β = 90 c = 198.48 γ = 90
Symmetry Space Group I 41 2 2
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 mirrors 2011-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9795 SSRL BL7-1
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 2.33 38.16 99.7 0.082 16.95 7 42332 42332
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 2.33 2.39 99.9 0.979 2.45 7.2 3074
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 (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 3RGA 2.33 38.16 42337 40197 2137 99.79 0.17887 0.17734 0.1849 0.20671 0.2089 RANDOM 56.566
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] 1.74 1.74 -3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.251 r_dihedral_angle_4_deg 20.519 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.125 r_angle_refined_deg 1.838 r_angle_other_deg 1.184 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.251 r_dihedral_angle_4_deg 20.519 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.125 r_angle_refined_deg 1.838 r_angle_other_deg 1.184 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4216 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 124
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling