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Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IRE PDB ENTRY 1IRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 30% PEG 400, 0.1M MES, 0.1M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.62 α = 90 b = 106.62 β = 90 c = 83.23 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 100 IMAGE PLATE RIGAKU RAXIS IV AXCO PX50 glass capillary optic with a 0.1mm focus 2004-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.52 20 0.091 16152
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 PDB ENTRY 1IRE 2.52 20 15851 831 93 0.20189 0.19814 0.195 0.27929 0.2734 RANDOM 28.171
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] -0.05 -0.05 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.799 r_dihedral_angle_4_deg 21.99 r_dihedral_angle_3_deg 20.582 r_dihedral_angle_1_deg 6.613 r_scangle_it 5.13 r_scbond_it 3.713 r_angle_refined_deg 2.189 r_mcangle_it 1.893 r_mcbond_it 1.722 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.799 r_dihedral_angle_4_deg 21.99 r_dihedral_angle_3_deg 20.582 r_dihedral_angle_1_deg 6.613 r_scangle_it 5.13 r_scbond_it 3.713 r_angle_refined_deg 2.189 r_mcangle_it 1.893 r_mcbond_it 1.722 r_nbtor_refined 0.32 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.215 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.159 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3488 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction HKL-2000 data scaling EPMR phasing