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CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE (point mutant 1) FROM PERMAFROST METAGENOMIC LIBRARY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QIN
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 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.14 α = 90 b = 92.18 β = 106.41 c = 74.46 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 2017-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 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 1.43 56.46 98 0.075 0.082 0.033 0.999 12.4 5.9 110412
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 1.43 1.45 95.2 0.959 1.06 0.443 0.626 5.5
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 6QIN 1.43 56.46 104774 5606 97.76 0.1576 0.1562 0.184 0.1904 RANDOM 18.001
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] 0.27 0.49 0.26 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.759 r_dihedral_angle_4_deg 20.935 r_dihedral_angle_3_deg 13.397 r_dihedral_angle_1_deg 6.234 r_angle_refined_deg 1.921 r_angle_other_deg 1.691 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.759 r_dihedral_angle_4_deg 20.935 r_dihedral_angle_3_deg 13.397 r_dihedral_angle_1_deg 6.234 r_angle_refined_deg 1.921 r_angle_other_deg 1.691 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4805 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction