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N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii complexed with its inhibitor MPG (phosphate-containing condition)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.4 M ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.1 41.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.821 α = 90 b = 77.821 β = 90 c = 229.23 γ = 120
Symmetry Space Group P 32 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 100 CCD RAYONIX MX-225 2015-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.90000 SPring-8 BL38B1
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 1.9 40 94.9 0.063 15.9 5.6 61101
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 1.9 1.93 95.5 0.49 2.6 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 29.46 57838 3087 94.61 0.22033 0.21765 0.26988 0.2449 RANDOM 35.608
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] 0.37 0.37 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 18.924 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 7.088 r_scangle_it 4.324 r_scbond_it 3.025 r_angle_refined_deg 1.986 r_mcangle_it 1.786 r_mcbond_it 1.124 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 18.924 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 7.088 r_scangle_it 4.324 r_scbond_it 3.025 r_angle_refined_deg 1.986 r_mcangle_it 1.786 r_mcbond_it 1.124 r_chiral_restr 0.144 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 6550 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling BSS data collection