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The E142L mutant of the amidase from Geobacillus pallidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 294 1.2M sodium citrate, 0.4M sodium chloride, 0.1M sodium acetate, pH 5.6, vapor diffusion, hanging drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.789 α = 90 b = 130.789 β = 90 c = 130.789 γ = 90
Symmetry Space Group P 42 3 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 CCD RIGAKU SATURN 944+ 2011-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.542
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 53.39 94.6 0.205 5 5.66 29066
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 1.97 93.7 0.516 2.3 5.09 2824
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 2PLQ 1.9 53.39 29045 1471 94.54 0.1958 0.1942 0.2042 0.2254 0.2322 RANDOM 14.5243
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 r_dihedral_angle_2_deg 33.494 r_dihedral_angle_4_deg 17.586 r_dihedral_angle_3_deg 13.762 r_dihedral_angle_1_deg 7.332 r_angle_refined_deg 2.008 r_angle_other_deg 0.951 r_chiral_restr 0.135 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.494 r_dihedral_angle_4_deg 17.586 r_dihedral_angle_3_deg 13.762 r_dihedral_angle_1_deg 7.332 r_angle_refined_deg 2.008 r_angle_other_deg 0.951 r_chiral_restr 0.135 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2649 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 1
Software Software Software Name Purpose d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction d*TREK data scaling