2VXQ | pdb_00002vxq

Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U6A	PDB ENTRIES 1U6A, 1WH0
experimental model	PDB	1WH0	PDB ENTRIES 1U6A, 1WH0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8		HANGING DROP DIFFUSION, 1 MICROL PROTEIN (IN 30 MM HEPES, 0.15 M NACL PH 6.8) MIXED WITH 1 MICROL RESERVOIR (20% PEG 3350, 0.2 M NAF)

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.437	α = 90
b = 105.437	β = 90
c = 110.225	γ = 90

Symmetry
Space Group	P 42 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	MARRESEARCH		2007-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	1.9	27.56	98.4	0.077	0.07	17.89	5.53		48722

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	1.9	1.92	89.5		0.24	2.43	4.34

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 ENTRIES 1U6A, 1WH0	1.9	30	48678	2466	98.3	0.179	0.177	0.18	0.226	0.23	RANDOM	21.76

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]
-0.08			-0.08		0.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.473
r_dihedral_angle_4_deg	19.1
r_dihedral_angle_3_deg	11.889
r_scangle_it	8.44
r_scbond_it	7.189
r_dihedral_angle_1_deg	7.088
r_mcangle_it	5.362
r_mcbond_it	4.763
r_angle_refined_deg	1.22
r_angle_other_deg	0.783
r_symmetry_hbond_refined	0.291
r_symmetry_vdw_refined	0.251
r_symmetry_vdw_other	0.225
r_nbd_other	0.2
r_nbd_refined	0.193
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.085
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_bond_other_d	0.003
r_gen_planes_refined	0.003
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	3967
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms

Software

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