2BK0 | pdb_00002bk0

Crystal structure of the major celery allergen Api G 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BV1	PDB ENTRY 1BV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5		VAPOUR DIFFUSION. RESERVOIR: 10% DIOXANE, 0.1M MES (PH 6.5), 1.6 M AMMONIUM SULFATE. PROTEIN: 35MG/ML IN 28 MM SODIUM PHOSPHATE (PH 7.0).

Crystal Properties
Matthews coefficient	Solvent content
2.5	35.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.878	α = 90
b = 67.947	β = 91.18
c = 48.001	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	277	IMAGE PLATE	MAR scanner 345 mm plate	OSMICS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ROTATING GENERATOR

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	2.8	36.96	90.1	0.09	8.3	1.65		7549

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	2.8	2.83	93		0.39	1.36	1.59

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 1BV1	2.9	30	6567	315	90	0.224	0.221	0.23	0.269	0.27	RANDOM	21.99

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]
-1.97		0.84	4.53		-2.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.961
r_dihedral_angle_4_deg	24.267
r_dihedral_angle_3_deg	19.527
r_dihedral_angle_1_deg	5.761
r_angle_refined_deg	1.053
r_angle_other_deg	0.941
r_scangle_it	0.575
r_symmetry_hbond_refined	0.378
r_scbond_it	0.346
r_mcangle_it	0.274
r_mcbond_it	0.243
r_nbd_refined	0.189
r_nbd_other	0.179
r_nbtor_refined	0.169
r_symmetry_vdw_other	0.162
r_xyhbond_nbd_refined	0.148
r_symmetry_vdw_refined	0.109
r_chiral_restr	0.102
r_nbtor_other	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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_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	2280
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing