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N-acetyl-B-D-glucoasminidase (GCNA) from Stretococcus gordonii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EPL PDB entry 2EPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 293 100mM Tris, 1.9M ammonium sulphate, 0.5%(v/v) PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.92 68.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.964 α = 90 b = 124.746 β = 90 c = 147.889 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2006-12-12 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 2.04 14.95 99.31 0.064 18.9 8.1 72240 71742 3 3 26.6
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 2.04 2.09 94.31 0.35 3.74 7.1
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 PDB entry 2EPL 2.04 14.95 72240 68128 3614 99.31 0.20091 0.20091 0.199 0.1866 0.23699 0.2173 RANDOM 40.635
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] -2.4 -1.41 3.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.656 r_dihedral_angle_4_deg 16.318 r_dihedral_angle_3_deg 12.946 r_scangle_it 6.591 r_dihedral_angle_1_deg 5.871 r_scbond_it 5.048 r_mcangle_it 3.145 r_mcbond_it 2.772 r_angle_refined_deg 1.245 r_angle_other_deg 0.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.656 r_dihedral_angle_4_deg 16.318 r_dihedral_angle_3_deg 12.946 r_scangle_it 6.591 r_dihedral_angle_1_deg 5.871 r_scbond_it 5.048 r_mcangle_it 3.145 r_mcbond_it 2.772 r_angle_refined_deg 1.245 r_angle_other_deg 0.764 r_mcbond_other 0.68 r_symmetry_vdw_refined 0.234 r_symmetry_vdw_other 0.233 r_nbd_refined 0.213 r_nbtor_refined 0.188 r_nbd_other 0.174 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.135 r_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4798 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling