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Human alpha-L-iduronidase in complex with iduronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W81 PDB ENTRY 3W81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 18%(w/v) PEG 3350, 0.18M K/Na tartrate, 3% (w/v)PEG MME 5000, 0.02M ammonium sulfate, 0.01M MES-Na, 7mM IdoA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 259.98 α = 90 b = 259.98 β = 90 c = 65.3 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 315r 2012-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.76 40 95.8 0.119 7.4 3.5 42253 40478 2 41.3
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 2.76 2.87 90.1 0.424 2.4 3.3 4781
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3W81 2.76 37.55 42270 38427 2042 95.74 0.19792 0.19498 0.1991 0.25431 0.2538 RANDOM 28.136
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] -1.16 -1.16 -1.16 3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.82 r_dihedral_angle_4_deg 15.767 r_dihedral_angle_3_deg 13.896 r_dihedral_angle_1_deg 5.631 r_angle_refined_deg 1.127 r_angle_other_deg 0.616 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.82 r_dihedral_angle_4_deg 15.767 r_dihedral_angle_3_deg 13.896 r_dihedral_angle_1_deg 5.631 r_angle_refined_deg 1.127 r_angle_other_deg 0.616 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 9770 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 381
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction Aimless data scaling