2H2T | pdb_00002h2t

CD23 Lectin domain, Calcium 2+-bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H2R	PDB ENTRY 2H2R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	17% (w/v) PEG 4000, 100 mM Mes buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
	20.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.31	α = 90
b = 51.261	β = 90
c = 58.768	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2004-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	1.02336	APS	32-ID

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	1.3	30	99.4	0.09	41.6	7.5	30523	30523			14.74

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	1.3	1.32	100		0.338	3.5	7.5	1515

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2H2R	1.3	38.63	28870	28870	1561	99.37	0.16953	0.16953	0.16785	0.18	0.20045	0.2	THIN SHELLS	15.865

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]
0.52			-0.56		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.961
r_sphericity_free	18.203
r_dihedral_angle_4_deg	17.542
r_dihedral_angle_3_deg	11.692
r_sphericity_bonded	7.9
r_scangle_it	7.473
r_dihedral_angle_1_deg	6.723
r_scbond_it	6.069
r_mcangle_it	5.828
r_mcbond_it	4.997
r_rigid_bond_restr	3.762
r_mcbond_other	3.363
r_angle_other_deg	2.527
r_angle_refined_deg	1.658
r_symmetry_vdw_other	0.4
r_xyhbond_nbd_other	0.251
r_symmetry_hbond_refined	0.237
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.227
r_nbd_other	0.222
r_xyhbond_nbd_refined	0.203
r_nbtor_refined	0.194
r_chiral_restr	0.099
r_nbtor_other	0.087
r_metal_ion_refined	0.031
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	1

Software

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