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Crystal structure of N370S Glucocerebrosidase at acidic pH.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 294 1M Ammonium Sulfate/0.2M Potassium Chloride/0.05M
Guanidine-Hydrochloride/0.1M Sodium Citrate, pH5.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.23 61.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.465 α = 90 b = 285.064 β = 90 c = 92.225 γ = 90
Symmetry Space Group C 2 2 21
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 2009-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 85 99.5 0.147 7.3 6.1 37753 37753 2 2 36.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.87 94.1 0.51 2.5 2.7
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 1OGS 2.7 50 37753 1997 99.53 0.17484 0.17197 0.1711 0.22921 0.2255 RANDOM 14.827
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] 1.84 -1.15 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.583 r_dihedral_angle_4_deg 20.759 r_dihedral_angle_3_deg 16.752 r_dihedral_angle_1_deg 6.697 r_scangle_it 4.14 r_scbond_it 2.558 r_angle_refined_deg 1.78 r_mcangle_it 1.505 r_mcbond_it 0.764 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.583 r_dihedral_angle_4_deg 20.759 r_dihedral_angle_3_deg 16.752 r_dihedral_angle_1_deg 6.697 r_scangle_it 4.14 r_scbond_it 2.558 r_angle_refined_deg 1.78 r_mcangle_it 1.505 r_mcbond_it 0.764 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7857 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 153
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling