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Crystal structure of beta-galactosidase from the psychrophilic Marinomonas ef1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 0.5 M NaCl, 100 mM Na-citrate, 2% ethylene imine polymer.
Crystal Properties Matthews coefficient Solvent content 4 69.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.332 α = 90 b = 133.332 β = 90 c = 232.574 γ = 120
Symmetry Space Group P 63 2 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 S 6M 2018-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.87313 ESRF ID14-4
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 1.9 116.29 100 0.255 10.9 29.4 96335
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 1.9 2 99.7 0.674 33.6
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 1KWG 1.9 116.29 87612 4630 95.79 0.164 0.1627 0.1763 0.1888 0.1993 RANDOM 20.48
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] 0.69 0.34 0.69 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 13.347 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_1_deg 5.989 r_angle_refined_deg 1.249 r_angle_other_deg 0.922 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 13.347 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_1_deg 5.989 r_angle_refined_deg 1.249 r_angle_other_deg 0.922 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5244 Nucleic Acid Atoms Solvent Atoms 999 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing