4OBR

Crystal structure of human alpha-L-iduronidase complex with alpha-L-iduronic acid

X-RAY DIFFRACTION

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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

Symmetry
Space Group	H 3

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	R-Free	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	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
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