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Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520, glucosamine complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 10mM glucosamine, 10 % PEG 6000, 0.1M HEPES-NaOH (pH 7.5), 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.16 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.294 α = 90 b = 102.59 β = 97.22 c = 89.804 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2011-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 50 99.5 0.079 19 3.6 88029
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 1.93 100 0.286 3.2 3.7
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 3H7L 1.9 28.9 83494 4417 99.2 0.16381 0.16167 0.1622 0.20379 0.2048 RANDOM 24.355
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] -0.06 0.02 0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.942 r_dihedral_angle_4_deg 14.849 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_1_deg 6.748 r_long_range_B_refined 6.003 r_scbond_it 3.354 r_mcangle_it 2.969 r_mcbond_it 2.185 r_angle_refined_deg 2.02 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.942 r_dihedral_angle_4_deg 14.849 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_1_deg 6.748 r_long_range_B_refined 6.003 r_scbond_it 3.354 r_mcangle_it 2.969 r_mcbond_it 2.185 r_angle_refined_deg 2.02 r_chiral_restr 0.156 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 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_it r_scangle_other 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 9132 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing