6Z32

Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GP0	Homology models of D7, 8, 9, 10, Crystal structure of D11 (1GP0)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.1 M MES pH 6.5, 1.6 M MgSO4, 10 mM mannose 6-phosphate

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.204	α = 90
b = 139.204	β = 90
c = 234.682	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER2 XE 16M		2013-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.05811	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	3.47	89.72	98.55	0.997	6.03	14.5		30224

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.47	3.59	98.43		0.127	0.84	14.9

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Homology models of D7, 8, 9, 10, Crystal structure of D11 (1GP0)	3.47	89.72	30215	1493	98.55	0.2607	0.3	RANDOM	197.426

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]
-0.15			-0.15		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.035
r_long_range_B_refined	25.876
r_long_range_B_other	25.876
r_scangle_other	16.286
r_dihedral_angle_3_deg	16.221
r_dihedral_angle_4_deg	15.811
r_mcangle_it	15.288
r_mcangle_other	15.288
r_scbond_it	10.345
r_scbond_other	10.344
r_mcbond_it	9.748
r_mcbond_other	9.739
r_dihedral_angle_1_deg	8.862
r_angle_refined_deg	1.564
r_angle_other_deg	1.242
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10358
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	191

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing
Coot	model building