☰ Navigation Tabs
Crystal structure of human alpha-L-iduronidase complex with alpha-L-iduronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MJ2 PDB ENTRY 4MJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.01 M HEPES, pH 7.5, 0.26 M sodium potassium tartrate, 20% PEG3350, 50 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 258.94 α = 90 b = 258.94 β = 90 c = 71.53 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 RAYONIX MX300HE collimating mirror with two stripes (Si, Rh/Pt) and toroidal focusing mirror (Rh/Pt) 2013-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97940 CLSI 08B1-1
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 2.46 48.94 97.8 0.085 12.89 3.6 64924 63496 -3
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) 1 2.46 2.524 82.8 0.389 3.43 2.82
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 (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 4MJ2 2.46 48.94 64924 60320 3175 97.79 0.20418 0.20232 0.23929 0.2237 RANDOM 39.549
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] -1.57 -1.57 -1.57 5.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.434 r_dihedral_angle_4_deg 15.949 r_dihedral_angle_3_deg 13.622 r_dihedral_angle_1_deg 6.261 r_angle_refined_deg 1.2 r_angle_other_deg 1.039 r_chiral_restr 0.066 r_bond_other_d 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.434 r_dihedral_angle_4_deg 15.949 r_dihedral_angle_3_deg 13.622 r_dihedral_angle_1_deg 6.261 r_angle_refined_deg 1.2 r_angle_other_deg 1.039 r_chiral_restr 0.066 r_bond_other_d 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9543 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 367
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling