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Pharmacological Chaperoning in Human alpha-Galactosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 293 PEG 8000, Sodium Cacodylate, Magnesium Chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.16 61.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.313 α = 90 b = 140.606 β = 90 c = 182.486 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 210 TOROIDAL FOCUSING MIRROR 2007-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.000 NSLS X6A
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 50 99.4 0.115 6.5 13.7 77091
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 2.07 96.1 0.782 10
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HG5 2.001 30.44 73158 3867 99.31 0.21119 0.20992 0.23436 0.2066 RANDOM 33.715
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] -0.05 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_3_deg 13.797 r_dihedral_angle_4_deg 11.718 r_scangle_it 8.59 r_scbond_it 6.014 r_dihedral_angle_1_deg 5.785 r_mcangle_it 4.002 r_mcbond_it 2.624 r_angle_refined_deg 1.231 r_mcbond_other 0.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_3_deg 13.797 r_dihedral_angle_4_deg 11.718 r_scangle_it 8.59 r_scbond_it 6.014 r_dihedral_angle_1_deg 5.785 r_mcangle_it 4.002 r_mcbond_it 2.624 r_angle_refined_deg 1.231 r_mcbond_other 0.996 r_angle_other_deg 0.852 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6244 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 294
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction