4A87

Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with naringenin.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A80	PDB ENTRY 4A80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		pH 7

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.65	α = 90
b = 55.42	β = 93.28
c = 37.89	γ = 90

Symmetry
Space Group	P 1 21 1

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	MIRRORS	2010-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	1.24	25.24	97.9	0.06	12.7	3.6		37419

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	1.24	1.31	88.4		0.17	5.2	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4A80	1.24	37.83	35510	1892	97.82	0.12826	0.1264	0.16238	RANDOM	14.134

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]
0.5		-0.25	0.76		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.156
r_dihedral_angle_2_deg	36.479
r_dihedral_angle_4_deg	31.394
r_sphericity_bonded	13.471
r_dihedral_angle_3_deg	12.535
r_scangle_it	6.338
r_dihedral_angle_1_deg	5.518
r_scbond_it	4.141
r_rigid_bond_restr	3.485
r_mcangle_it	3.186
r_mcbond_it	2.035
r_angle_refined_deg	1.698
r_angle_other_deg	0.926
r_symmetry_vdw_refined	0.293
r_nbd_refined	0.284
r_symmetry_vdw_other	0.238
r_nbd_other	0.204
r_xyhbond_nbd_refined	0.2
r_symmetry_hbond_refined	0.2
r_metal_ion_refined	0.198
r_nbtor_refined	0.188
r_chiral_restr	0.109
r_nbtor_other	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1225
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing