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Crystal structure of hyperthermophilic nitrilase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J31 1j31.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 35% PEG 550MME, 0.2M MgCl2, 0.2M TrisHCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.174 α = 90 b = 59.174 β = 90 c = 127.22 γ = 90
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 ADSC QUANTUM 315r 2006-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.57 50 83.6 0.068 0.068 11.8 5.5 51424
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.59 16 0.193 0.193 1.7 1.4 984
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 1j31.pdb 1.57 25.91 48714 1055 81.76 0.13235 0.13136 0.1323 0.17591 0.1723 RANDOM 23.829
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] -11.83 -11.83 23.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_4_deg 20.076 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_1_deg 6.824 r_scangle_it 3.982 r_scbond_it 2.445 r_angle_refined_deg 1.533 r_mcangle_it 1.454 r_mcbond_it 0.845 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_4_deg 20.076 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_1_deg 6.824 r_scangle_it 3.982 r_scbond_it 2.445 r_angle_refined_deg 1.533 r_mcangle_it 1.454 r_mcbond_it 0.845 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4178 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling