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Crystal structure of mouse nitrilase-2 at 1.4A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F89 PDB ENTRY 1F89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 250 MM CACL2 100 MM HEPES PH 8.0 30% V/V PEG MME 550 12 MG/ML PROTEIN
Crystal Properties Matthews coefficient Solvent content 3.64 66.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.268 α = 90 b = 90.268 β = 90 c = 54.059 γ = 120
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 1.49 78.09 99.9 0.03 41.35 2.7 76281 2
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 1.49 1.53 100 0.28 2.57 1.8
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 1F89 1.49 78.09 76281 4037 99.9 0.144 0.142 0.1597 0.177 0.1714 RANDOM 10.23
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] 0.24 0.12 0.24 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_3_deg 11.745 r_dihedral_angle_4_deg 11.643 r_dihedral_angle_1_deg 6.323 r_scangle_it 2.809 r_scbond_it 2.065 r_mcangle_it 1.327 r_angle_refined_deg 1.305 r_mcbond_it 1.12 r_angle_other_deg 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_3_deg 11.745 r_dihedral_angle_4_deg 11.643 r_dihedral_angle_1_deg 6.323 r_scangle_it 2.809 r_scbond_it 2.065 r_mcangle_it 1.327 r_angle_refined_deg 1.305 r_mcbond_it 1.12 r_angle_other_deg 0.84 r_nbd_refined 0.203 r_nbd_other 0.196 r_symmetry_vdw_refined 0.179 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_other 0.156 r_xyhbond_nbd_refined 0.134 r_nbtor_other 0.083 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing