2YHF | pdb_00002yhf

1.9 Angstrom Crystal Structure of CLEC5A

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K9J	PDB ENTRIES 1K9J, 3BDW, 1E87, 2IT5, 3BC6.
experimental model	PDB	3BDW	PDB ENTRIES 1K9J, 3BDW, 1E87, 2IT5, 3BC6.
experimental model	PDB	1E87	PDB ENTRIES 1K9J, 3BDW, 1E87, 2IT5, 3BC6.
experimental model	PDB	2IT5	PDB ENTRIES 1K9J, 3BDW, 1E87, 2IT5, 3BC6.
experimental model	PDB	3BC6	PDB ENTRIES 1K9J, 3BDW, 1E87, 2IT5, 3BC6.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		100MM TRIS PH8.0, 30% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.109	α = 90
b = 109.109	β = 90
c = 84.879	γ = 120

Symmetry
Space Group	P 31

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	MARMOSAIC 225 mm CCD	RH COATED COLLIMATING MIRROR	2007-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1		SRS	PX10.1

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	1.9	50	87.1	0.07	12.9	2.9		88632		0.01

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	1.9	1.97	76.4		0.5	1.62	2.4

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1K9J, 3BDW, 1E87, 2IT5, 3BC6.	1.9	94.49	73334	3883	87.15	0.219	0.2164	0.22	0.26727	0.27	RANDOM	22.408

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]
0.66	0.33		0.66		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.001
r_dihedral_angle_4_deg	17.923
r_dihedral_angle_3_deg	13.182
r_dihedral_angle_1_deg	6.2
r_scangle_it	1.515
r_scbond_it	0.949
r_angle_refined_deg	0.947
r_mcangle_it	0.769
r_mcbond_it	0.44
r_nbtor_refined	0.299
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.164
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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	8748
Nucleic Acid Atoms
Solvent Atoms	940
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing
MOLREP	phasing
REFMAC	refinement