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Crystal structure of thermostable, organic-solvent tolerant lipase from Geobacillus sp. strain ARM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DSN pdb entry 2DSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 293 0.1M MES monohydrate, 12% v/v PEG 20000, pH 6.5, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.786 α = 90 b = 143.392 β = 105.88 c = 63.965 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 225 mm CCD 2011-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.48 50 98 0.114 12.5 3.9 42814 42814 5 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2DSN 2.3 50 42814 40490 2152 99.45 0.17627 0.17275 0.24165 0.2256 RANDOM 37.167
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] 2.87 -1.05 -1.46 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.579 r_dihedral_angle_4_deg 16.764 r_dihedral_angle_3_deg 15.814 r_dihedral_angle_1_deg 6.534 r_scangle_it 4.713 r_scbond_it 3.021 r_angle_refined_deg 1.854 r_mcangle_it 1.849 r_mcbond_it 1.007 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.579 r_dihedral_angle_4_deg 16.764 r_dihedral_angle_3_deg 15.814 r_dihedral_angle_1_deg 6.534 r_scangle_it 4.713 r_scbond_it 3.021 r_angle_refined_deg 1.854 r_mcangle_it 1.849 r_mcbond_it 1.007 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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 6016 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling