2H2R

Crystal structure of the human CD23 Lectin domain, apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV8	A MODIFIED VERSION OF PDB ENTRY 1DV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	1.2 M sodium monobasic phosphate, 0.8 M potassium dibasic phosphate, 0.1 M Caps buffer pH 10.5, and 0.2 M lithium sulfate; final pH 6.2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.354	α = 90
b = 50.667	β = 127.09
c = 75.061	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	MARRESEARCH		2003-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.97895	APS	5ID-B

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	1.5	30	99.5	0.051	18.7	7	53947	53947			24.6

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)
	1.5	1.66	99.8		0.281	6.3	7.4	14045

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	A MODIFIED VERSION OF PDB ENTRY 1DV8	1.5	59.87	51219	51219	2727	99.85	0.12562	0.12562	0.12353	0.16481	THIN SHELLS	20.547

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]
-0.71		-0.46	0.24		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.505
r_sphericity_free	22.32
r_dihedral_angle_3_deg	13.568
r_dihedral_angle_4_deg	12.903
r_scangle_it	9.247
r_sphericity_bonded	8.995
r_scbond_it	7.468
r_mcangle_it	7.01
r_dihedral_angle_1_deg	6.771
r_mcbond_it	6.33
r_rigid_bond_restr	4.669
r_mcbond_other	3.966
r_angle_refined_deg	1.449
r_angle_other_deg	0.768
r_symmetry_vdw_other	0.269
r_nbd_other	0.222
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.219
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.183
r_symmetry_vdw_refined	0.182
r_chiral_restr	0.11
r_nbtor_other	0.094
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2193
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
CNS	phasing