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Crystal Structure of the ternary complex of lipase from Thermomyces lanuginosa with Ethylacetoacetate and P-nitrobenzaldehyde at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M HEPES, 0.1M Nacl, 1.6M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.9 68.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.461 α = 90 b = 140.461 β = 90 c = 80.289 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH Mirror 2013-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 2.3 121.67 99.5 0.072 41.5 40215
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 2.3 2.34 99.4 0.305 4
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 MOLECULAR REPLACEMENT THROUGHOUT 4DYH 2.3 50 40215 37933 2051 99.39 0.22328 0.22328 0.22096 0.2278 0.26583 0.2649 RANDOM 47.494
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] 23.01 23.01 -46.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.777 r_dihedral_angle_4_deg 18.94 r_dihedral_angle_3_deg 17.227 r_dihedral_angle_1_deg 7.979 r_angle_refined_deg 2.081 r_angle_other_deg 1.09 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.777 r_dihedral_angle_4_deg 18.94 r_dihedral_angle_3_deg 17.227 r_dihedral_angle_1_deg 7.979 r_angle_refined_deg 2.081 r_angle_other_deg 1.09 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4142 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling