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Crystal structure of the human N-acetyl-alpha-glucosaminidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 1.0 M lithium sulfate, 0.01 M nickel chloride, 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 5.94 79.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.088 α = 90 b = 205.088 β = 90 c = 78.398 γ = 120
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 315 2010-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.32 100 100 0.086 20.7 9.5 81740 45.2
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 2.32 2.4 99.8 0.763 1.85 5.8
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 2VCC 2.32 100 77480 3993 99.56 0.1669 0.16591 0.1725 0.18579 0.1899 RANDOM 53.533
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] 0.07 0.04 0.07 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.31 r_dihedral_angle_4_deg 19.703 r_dihedral_angle_3_deg 18.275 r_dihedral_angle_1_deg 6.162 r_long_range_B_refined 5.717 r_long_range_B_other 5.695 r_scangle_other 3.779 r_scbond_it 2.375 r_scbond_other 2.374 r_mcangle_it 2.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.31 r_dihedral_angle_4_deg 19.703 r_dihedral_angle_3_deg 18.275 r_dihedral_angle_1_deg 6.162 r_long_range_B_refined 5.717 r_long_range_B_other 5.695 r_scangle_other 3.779 r_scbond_it 2.375 r_scbond_other 2.374 r_mcangle_it 2.239 r_mcangle_other 2.239 r_angle_refined_deg 1.776 r_mcbond_other 1.461 r_mcbond_it 1.46 r_angle_other_deg 1.11 r_chiral_restr 0.127 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5693 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data scaling PHASER phasing HKL-2000 data reduction