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Leukotriene A4 hydrolase complexed with inhibitor RB3041
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 298 Co-crystallized with LTA4H by liquid-liquid diffusion in melting-point capillaries. A Tris-buffered (10 mM, pH 7.5) solution of protein and inhibitor in approximately equimolar concentrations (~70 microM) was layered on the precipitate solution containing 28% (weight/volume) polyethylene glycol (Mw 8000), 50 mM Na acetate, 100 mM imidazole, pH 6.8, and 5 mM YbCl3, LIQUID DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.21 α = 90 b = 87.23 β = 90 c = 99.23 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2005-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.97 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.89 65.515 97.5 0.078 0.078 6.2 5.7 53141 53141 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.89 2 94.9 0.26 0.26 2.7 5.7 7434
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT pdb entry1H19 1.89 14.85 53091 53091 1763 97.17 0.176 0.176 0.175 0.174 0.227 0.2276 RANDOM 28.108
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] 0.11 -2.22 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.46 r_dihedral_angle_4_deg 18.82 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_1_deg 6.086 r_scangle_it 4.505 r_scbond_it 3.007 r_mcangle_it 1.863 r_angle_refined_deg 1.717 r_mcbond_it 1.24 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.46 r_dihedral_angle_4_deg 18.82 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_1_deg 6.086 r_scangle_it 4.505 r_scbond_it 3.007 r_mcangle_it 1.863 r_angle_refined_deg 1.717 r_mcbond_it 1.24 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.156 r_metal_ion_refined 0.141 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4877 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 37
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XSCALE data scaling XFIT data reduction