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CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE FROM PERMAFROST METAGENOMIC LIBRARY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 250mM Magnesium chloride, 12-18% PEG3350, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.01 α = 90 b = 92.35 β = 106.83 c = 74.23 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 PIXEL DECTRIS PILATUS3 6M 2016-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.6 56.31 97.4 0.14 0.153 0.061 0.985 7.8 6.1 77747
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 1.6 1.63 95.9 0.653 0.716 0.288 0.833 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3L1H 1.6 56.31 73837 3883 97.25 0.1585 0.157 0.1866 0.2105 RANDOM 18.076
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] 0.42 0.82 -0.13 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.749 r_dihedral_angle_4_deg 21.213 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 6.436 r_angle_refined_deg 2.299 r_angle_other_deg 2.189 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.749 r_dihedral_angle_4_deg 21.213 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 6.436 r_angle_refined_deg 2.299 r_angle_other_deg 2.189 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4731 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 3
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction