4B9R | pdb_00004b9r

Crystal structure of the Major Birch Pollen Allergen Bet v 1.0101 (isoform a) nitrated in vitro with tetranitromethan.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A8U	PDB ENTRY 4A8U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		2M AMMONIUM SULFATE 1.5% 2-METHYL-2,4-PENTANDIOL, pH 7

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.41	α = 90
b = 55.14	β = 92.77
c = 37.61	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	ADSC QUANTUM 315r		2011-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.76	37.57	95.9	0.06	12.7	3.5		12627		3	20.1

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	1.76	1.86	92.3		0.4	3.1	3.3

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 ENTRY 4A8U	1.76	37.57	11984	625	95.38	0.16824	0.16418	0.17	0.24913	0.25	RANDOM	19.716

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]
0.58		0.07	-0.31		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_mcbond_other	1483.8
r_dihedral_angle_2_deg	37.31
r_sphericity_free	35.496
r_dihedral_angle_4_deg	21.387
r_dihedral_angle_3_deg	13.853
r_mcangle_it	10.104
r_sphericity_bonded	9.321
r_mcbond_it	7.695
r_dihedral_angle_1_deg	5.21
r_rigid_bond_restr	1.596
r_angle_refined_deg	1.281
r_angle_other_deg	0.861
r_nbd_refined	0.391
r_symmetry_vdw_refined	0.245
r_nbd_other	0.238
r_symmetry_vdw_other	0.206
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.135
r_symmetry_hbond_refined	0.095
r_nbtor_other	0.087
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	1230
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	5

Software

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