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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 PDB 2EPK PDB entry 2EPK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100mM HEPES, 2M ammonium sulphate, 0.5%(v/v) PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.574 α = 90 b = 112.332 β = 90 c = 103.127 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate mirror 2006-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.61 15.02 99.34 0.064 20.9 9.1 162103 161033 3 3 18.2
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 1.61 1.65 94.37 0.5 3.51 8.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2EPK 1.61 15.02 162103 161033 8028 99.34 0.16912 0.16912 0.1674 0.20186 0.2188 RANDOM 19.952
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] 1.03 -0.23 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 12.09 r_dihedral_angle_1_deg 5.853 r_scangle_it 5.594 r_scbond_it 4.056 r_mcangle_it 2.577 r_mcbond_it 2.347 r_angle_refined_deg 1.33 r_angle_other_deg 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 12.09 r_dihedral_angle_1_deg 5.853 r_scangle_it 5.594 r_scbond_it 4.056 r_mcangle_it 2.577 r_mcbond_it 2.347 r_angle_refined_deg 1.33 r_angle_other_deg 0.805 r_mcbond_other 0.586 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.194 r_nbtor_refined 0.185 r_nbd_other 0.178 r_symmetry_vdw_other 0.172 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.105 r_nbtor_other 0.082 r_chiral_restr 0.081 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 10132 Nucleic Acid Atoms Solvent Atoms 777 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling