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A mutant of the nitrile hydratase from Geobacillus pallidus having enhanced thermostability
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 30% PEG400, 100mM magnesium chloride, 100mM MES (2[N-Morpholino]ethanesulfonic acid), 10-40mg/ml protein, pH 6.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.832 α = 90 b = 105.832 β = 90 c = 83.723 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 225 mm CCD mirrors 2007-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.979 ESRF BM14
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 1.16 26.99 99.6 0.047 5.58 162627
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) 1.16 1.2 100 0.3 4.1 5.41 16139
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 2dpp 1.16 26.99 162458 8144 99.49 0.128 0.127 0.144 0.1672 RANDOM 15.944
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.797 r_dihedral_angle_4_deg 17.36 r_sphericity_free 15.306 r_dihedral_angle_3_deg 11.94 r_scangle_it 6.806 r_dihedral_angle_1_deg 6.148 r_sphericity_bonded 5.946 r_scbond_it 5.032 r_mcangle_it 3.467 r_rigid_bond_restr 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.797 r_dihedral_angle_4_deg 17.36 r_sphericity_free 15.306 r_dihedral_angle_3_deg 11.94 r_scangle_it 6.806 r_dihedral_angle_1_deg 6.148 r_sphericity_bonded 5.946 r_scbond_it 5.032 r_mcangle_it 3.467 r_rigid_bond_restr 2.686 r_mcbond_it 2.536 r_angle_refined_deg 1.726 r_mcbond_other 1.324 r_angle_other_deg 0.986 r_chiral_restr 0.113 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 3506 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 3
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection d*TREK data reduction