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Leukotriene A4 hydrolase in complex with fragment 3-(benzyloxy)pyridin-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FH7 PDB entry 3FH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 13% PEG 8000, 100 mM Imidazole pH 6.5, 100 mM Na Acetate, 5 mM YbCl3, crystal soaked in 13% PEG 8000, 100 mM Imidazole, 100 mM Sodium Acetate, 150 mM NaCl, soak with 5 mM 3-(benzyloxy)pyridin-2-amine, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.148 α = 90 b = 87.079 β = 90 c = 99.239 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 RIGAKU SATURN 944 2008-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.15 50 98.1 0.185 5.9 3 36802
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) 2.15 2.23 88.9 0.538 2
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 3FH7 2.15 50 36758 1835 0.208 0.206 0.2012 0.257 0.2513 RANDOM 17.02
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] 0.28 -0.97 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.466 r_dihedral_angle_4_deg 16.46 r_dihedral_angle_3_deg 14.148 r_dihedral_angle_1_deg 5.95 r_scangle_it 2.824 r_scbond_it 1.744 r_angle_refined_deg 1.279 r_mcangle_it 0.893 r_mcbond_it 0.479 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.466 r_dihedral_angle_4_deg 16.46 r_dihedral_angle_3_deg 14.148 r_dihedral_angle_1_deg 5.95 r_scangle_it 2.824 r_scbond_it 1.744 r_angle_refined_deg 1.279 r_mcangle_it 0.893 r_mcbond_it 0.479 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4844 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 39
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling