3CYZ | pdb_00003cyz

Dimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with 9-keto-2(E)-decenoic acid at pH 7.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BJH	PDB ENTRY 3BJH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.2M magnesium chloride, 0.1M Tris, 15% PEG8000, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.285	α = 90
b = 75.555	β = 90
c = 84.113	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	cylindrical gazing incidence mirror	2007-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.979	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	1.8	84.25	96.4	0.091	0.091	16.9	6.9	21263	21263			17.97

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	1.8	1.9	84.1		0.457	0.457	3.7	6.9	2614

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 ENTRY 3BJH	1.8	20	20184	20184	1057	96.03	0.16372	0.16372	0.16181	0.18	0.19964	0.21	RANDOM	16.682

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]
2.1			-1.69		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.804
r_dihedral_angle_3_deg	14
r_dihedral_angle_4_deg	10.937
r_dihedral_angle_1_deg	4.836
r_scangle_it	2.654
r_scbond_it	1.835
r_angle_refined_deg	1.413
r_angle_other_deg	1.028
r_mcangle_it	0.965
r_mcbond_it	0.799
r_nbd_refined	0.239
r_mcbond_other	0.209
r_nbd_other	0.204
r_symmetry_vdw_other	0.202
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.16
r_nbtor_other	0.091
r_chiral_restr	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1784
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	56

Software

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