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Crystal structure of a type III secretion system protein complexed with the lipid, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y9L PDB ENTRY 1Y9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 (NH3)2SO4 LiSO4 NaCHOCH3, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.036 α = 90 b = 49.721 β = 101.99 c = 29.52 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MARRESEARCH MIRRORS 2004-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.87 42.4 96.37 0.027 34 4.6 9460 9460 32.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.94 93.6 0.22 6.2 3.9 912
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1Y9L 1.87 42.4 9301 8964 496 96.37 0.20843 0.20843 0.20613 0.24907 0.2774 EQUIVALENT RFREE REFLECTIONS TO PDB ENTRY 1Y9L (RANDOM) 33.85
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] -0.35 -0.07 0.7 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_3_deg 15.501 r_dihedral_angle_4_deg 11.05 r_dihedral_angle_1_deg 6.918 r_scangle_it 3.603 r_scbond_it 2.268 r_mcangle_it 1.531 r_angle_refined_deg 1.473 r_mcbond_it 0.976 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_3_deg 15.501 r_dihedral_angle_4_deg 11.05 r_dihedral_angle_1_deg 6.918 r_scangle_it 3.603 r_scbond_it 2.268 r_mcangle_it 1.531 r_angle_refined_deg 1.473 r_mcbond_it 0.976 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.253 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 870 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling