4KGJ

Crystal structure of human alpha-L-iduronidase complex with 5-fluoro-alpha-L-idopyranosyluronic acid fluoride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JXOPDB ENTRY 4JXO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.01 M HEPES, pH 7.5, 0.26 M sodium potassium tartrate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2962.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 259.343α = 90
b = 259.343β = 90
c = 71.379γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS 6MRh coated flat mirror2013-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.9938.0599.70.18811.7563618836079-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.993.199.90.743.356.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4JXO2.9938.053437734274180399.70.179970.177540.22689RANDOM39.848
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]
-2.13-2.13-2.136.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.419
r_dihedral_angle_4_deg18.556
r_dihedral_angle_3_deg15.387
r_dihedral_angle_1_deg5.63
r_mcangle_it2.27
r_scbond_it1.329
r_mcbond_it1.282
r_angle_refined_deg1.109
r_chiral_restr0.068
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.419
r_dihedral_angle_4_deg18.556
r_dihedral_angle_3_deg15.387
r_dihedral_angle_1_deg5.63
r_mcangle_it2.27
r_scbond_it1.329
r_mcbond_it1.282
r_angle_refined_deg1.109
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.004
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_mcangle_other
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 AtomsNumber
Protein Atoms9551
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms341

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling