2AS8 | pdb_00002as8

Crystal structure of mature and fully active Der p 1 allergen

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PCK	PDB ID 7PCK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Low salt	4.5	277	25mM sodium acetate, pH 4.5, Low salt, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.12	α = 90
b = 78.43	β = 90
c = 83.774	γ = 90

Symmetry
Space Group	P 21 21 2

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 210	channel-cut silicon monochromator, toroidally bent cylindrical grazing incidence mirror. Two monochromator crystals Si(311) cut and a lower resolution Si(111) cut.	2004-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.006768	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	50	98.3	0.117	0.1		34	36029	42045		-2	22.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.89	95.2	95.2	0.574	0.429	3	7.5	2476

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 ID 7PCK	1.95	28.6	36177	34344	1832	98.42	0.191	0.18819	0.18492	0.2	0.25171	0.19	RANDOM	21.39

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]
-2.31			3.73		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.2
r_dihedral_angle_4_deg	19.99
r_dihedral_angle_3_deg	16.975
r_dihedral_angle_1_deg	6.283
r_scangle_it	3.927
r_scbond_it	2.982
r_angle_refined_deg	1.999
r_mcbond_it	1.519
r_mcangle_it	1.399
r_angle_other_deg	1.192
r_symmetry_vdw_refined	0.519
r_chiral_restr	0.491
r_symmetry_vdw_other	0.424
r_symmetry_hbond_refined	0.384
r_nbd_refined	0.232
r_nbd_other	0.228
r_xyhbond_nbd_refined	0.214
r_nbtor_refined	0.183
r_mcbond_other	0.169
r_nbtor_other	0.095
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.007
r_gen_planes_other	0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3520
Nucleic Acid Atoms
Solvent Atoms	791
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction