2BPD | pdb_00002bpd

STRUCTURE OF MURINE DECTIN-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K9J	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87
experimental model	PDB	1FM5	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87
experimental model	PDB	1HQ8	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87
experimental model	PDB	1JA3	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87
experimental model	PDB	1MPU	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87
experimental model	PDB	1E87	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2 M DI-AMMONIUM HYDROGEN CITRATE, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.104	α = 90
b = 57.104	β = 90
c = 73.422	γ = 120

Symmetry
Space Group	P 32

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 CCD	TOROIDAL MIRROR	2004-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.5	30	97	0.05	28.1	4.8		41593		-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	1.5	1.55	78.1		0.57	1.7	3.1

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87	1.5	30	39882	1677	97	0.216	0.214	0.21	0.27	RANDOM	30.53

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]
0.4	0.2		0.4		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.973
r_dihedral_angle_4_deg	19.806
r_dihedral_angle_3_deg	14.3
r_dihedral_angle_1_deg	6.684
r_scangle_it	2.793
r_scbond_it	1.986
r_angle_refined_deg	1.336
r_mcangle_it	1.273
r_mcbond_it	0.821
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.235
r_symmetry_hbond_refined	0.205
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_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	2083
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CaspR	phasing
AMoRE	phasing
REFMAC	refinement