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N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other accompanying SeMet structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.1 293 100mM Tris, 2M ammonium sulphate, 2 %(v/v) PEG400, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.93 68.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.561 α = 90 b = 124.535 β = 90 c = 147.793 γ = 90
Symmetry Space Group I 2 2 2
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 MARRESEARCH 2006-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97928 APS 23-ID-D
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 1.4 29.4 99.88 0.09 17.8 9.8 222135 221868 3 3 18.5
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 1.4 1.44 99.39 0.5 2.53 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 accompanying SeMet structure 1.4 29.39 221868 210780 11088 99.88 0.18699 0.18699 0.18635 0.1875 0.19905 0.1977 RANDOM 20.709
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] -1.8 -1.09 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 11.834 r_dihedral_angle_1_deg 5.79 r_scangle_it 5.594 r_scbond_it 4.052 r_mcangle_it 2.574 r_mcbond_it 2.338 r_angle_refined_deg 1.304 r_angle_other_deg 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 11.834 r_dihedral_angle_1_deg 5.79 r_scangle_it 5.594 r_scbond_it 4.052 r_mcangle_it 2.574 r_mcbond_it 2.338 r_angle_refined_deg 1.304 r_angle_other_deg 0.814 r_mcbond_other 0.492 r_symmetry_vdw_other 0.251 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.212 r_nbtor_refined 0.185 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.08 r_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4992 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling