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Y233A-Investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase GIM-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YNT PDB ENTRY 2YNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 28% PEG 4000, 0.1 M HEPES PH 7.0 AND POTASSIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 1.88 34.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.434 α = 90 b = 131.222 β = 94.83 c = 40.842 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 PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.46 44 98.4 0.04 12.2 3.8 68700 19.12
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 1.46 1.54 95.8 0.46 2.2 3.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2YNT 1.459 24.914 1.37 68632 2080 98.41 0.1292 0.128 0.13 0.1671 0.1676 17.4
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 12.706 f_angle_d 0.995 f_chiral_restr 0.06 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3375 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing