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Crystal structure of MGS-M2, an alpha/beta hydrolase enzyme from a Medee basin deep-sea metagenome library
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CR6 PDB entry 1CR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 protein treated with thermolysin in 1/10 molar ratio crystallization in: 0.1 M sodium Hepes, 1.4 M sodium citrate, cryoprotectant: 15% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.99 58.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.568 α = 90 b = 139.134 β = 89.94 c = 111.109 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 IMAGE PLATE RIGAKU RAXIS IV++ 2014-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 3 32 99.9 0.093 17.08 4.6 63183 -2
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 3 3.05 100 0.536 3.66 4.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1CR6 3.01 31.669 1.34 63067 1992 99.2 0.2029 0.2012 0.2554 0.2108
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.686 f_angle_d 0.711 f_chiral_restr 0.029 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17910 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 12
Software Software Software Name Purpose StructureStudio data collection PHENIX model building PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing