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Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 440min at 293K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZPB PDB ENTRY 2ZPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 8000, 0.1M Tris-HCl pH 7.5, 300mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.046 α = 90 b = 60.23 β = 125.12 c = 81.48 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2006-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.491 66.667 93.8 69072
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 2ZPB 1.491 8 65146 3466 93.81 0.15822 0.15694 0.1561 0.18221 0.1817 RANDOM 14.105
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 35.157 r_dihedral_angle_4_deg 17.347 r_dihedral_angle_3_deg 11.168 r_dihedral_angle_1_deg 5.238 r_scangle_it 2.706 r_scbond_it 1.62 r_angle_refined_deg 1.101 r_mcangle_it 1.019 r_mcbond_it 0.609 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_dihedral_angle_4_deg 17.347 r_dihedral_angle_3_deg 11.168 r_dihedral_angle_1_deg 5.238 r_scangle_it 2.706 r_scbond_it 1.62 r_angle_refined_deg 1.101 r_mcangle_it 1.019 r_mcbond_it 0.609 r_nbtor_refined 0.321 r_symmetry_hbond_refined 0.287 r_nbd_refined 0.249 r_xyhbond_nbd_refined 0.182 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.076 r_metal_ion_refined 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_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 3183 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing