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Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 120min 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 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.083 α = 90 b = 60.112 β = 125.03 c = 81.699 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 1.387 66.965 98 89589 14.2
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 1.39 7.98 84855 4463 98.14 0.17334 0.17215 0.1712 0.19612 0.1944 RANDOM 17.121
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 32.939 r_dihedral_angle_4_deg 18.032 r_dihedral_angle_3_deg 10.867 r_dihedral_angle_1_deg 5.228 r_scangle_it 2.382 r_scbond_it 1.548 r_angle_refined_deg 1.181 r_mcangle_it 1.01 r_mcbond_it 0.652 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.939 r_dihedral_angle_4_deg 18.032 r_dihedral_angle_3_deg 10.867 r_dihedral_angle_1_deg 5.228 r_scangle_it 2.382 r_scbond_it 1.548 r_angle_refined_deg 1.181 r_mcangle_it 1.01 r_mcbond_it 0.652 r_nbtor_refined 0.31 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.134 r_xyhbond_nbd_refined 0.115 r_metal_ion_refined 0.091 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 3249 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing