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Crystal structure of a thermostable lipase from Marine Streptomyces
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 1.0M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic (pH 5.0)
Crystal Properties Matthews coefficient Solvent content 3.85 68.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.5 α = 90 b = 129.5 β = 90 c = 137.83 γ = 120
Symmetry Space Group P 32 2 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 ADSC QUANTUM 315r 2015-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.34 64.75 99.2 0.099 0.104 0.032 0.998 15.4 10.5 56185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.41 98.8 0.929 0.977 0.3 0.821 10.4 4533
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 5H6B 2.34 64.76 53333 2850 99.02 0.1929 0.1914 0.1971 0.2216 0.2258 RANDOM 42.999
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] 0.47 0.23 0.47 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_4_deg 19.727 r_dihedral_angle_3_deg 15.489 r_dihedral_angle_1_deg 6.465 r_mcangle_it 3.709 r_mcbond_it 2.402 r_mcbond_other 2.401 r_angle_refined_deg 1.53 r_angle_other_deg 1.003 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_4_deg 19.727 r_dihedral_angle_3_deg 15.489 r_dihedral_angle_1_deg 6.465 r_mcangle_it 3.709 r_mcbond_it 2.402 r_mcbond_other 2.401 r_angle_refined_deg 1.53 r_angle_other_deg 1.003 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5731 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction