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Crystal structure of lipase TrLipB from Thermomocrobium roseum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1M Succinic acid,0.1M HEPES,7,1% w/vPEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.402 α = 90 b = 129.402 β = 90 c = 122.792 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2021-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 45.75 100 0.082 22.8 14.4 70819
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) 1 2 2.04 0.821
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1lzk 2 45.75 70744 3497 99.983 0.159 0.1572 0.1695 0.1862 0.1984 39.58
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] -1.717 -1.717 3.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.203 r_dihedral_angle_4_deg 19.61 r_dihedral_angle_3_deg 12.394 r_lrange_it 7.089 r_lrange_other 7 r_dihedral_angle_1_deg 6.212 r_scangle_it 5.397 r_scangle_other 5.396 r_mcangle_it 3.596 r_mcangle_other 3.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.203 r_dihedral_angle_4_deg 19.61 r_dihedral_angle_3_deg 12.394 r_lrange_it 7.089 r_lrange_other 7 r_dihedral_angle_1_deg 6.212 r_scangle_it 5.397 r_scangle_other 5.396 r_mcangle_it 3.596 r_mcangle_other 3.596 r_scbond_it 3.562 r_scbond_other 3.561 r_mcbond_it 2.593 r_mcbond_other 2.592 r_angle_refined_deg 1.454 r_angle_other_deg 1.319 r_nbd_other 0.259 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.161 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4948 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing