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N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the presence of cadmium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1M Tris-HCl (pH 8.0), 0.2M MgCl2, 3.0M 1,6-hexanediol, 5mM CdCl2
Crystal Properties Matthews coefficient Solvent content 4.04 69.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.895 α = 74.69 b = 93.88 β = 74.68 c = 93.877 γ = 74.68
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 315 2013-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.99522 SPring-8 BL38B1
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 1.51 50 95.2 15.8 1.9 435340
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 3WL4 1.51 31.16 413484 21852 95.65 0.1526 0.15183 0.1524 0.16714 0.1672 RANDOM 21.222
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] -0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.845 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 12.683 r_scangle_it 6.314 r_dihedral_angle_1_deg 5.907 r_scbond_it 4.034 r_angle_refined_deg 2.911 r_mcangle_it 2.606 r_mcbond_it 1.595 r_chiral_restr 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.845 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 12.683 r_scangle_it 6.314 r_dihedral_angle_1_deg 5.907 r_scbond_it 4.034 r_angle_refined_deg 2.911 r_mcangle_it 2.606 r_mcbond_it 1.595 r_chiral_restr 0.214 r_bond_refined_d 0.035 r_gen_planes_refined 0.017 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_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 13140 Nucleic Acid Atoms Solvent Atoms 1412 Heterogen Atoms 466
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing