3FE9 | pdb_00003fe9

Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand soaked at pH 7.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H8V	PDB ENTRY 2H8V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	1.7M ammonium sulfate, 0.1M sodium citrate, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.298	α = 90
b = 83.909	β = 90
c = 46.804	γ = 90

Symmetry
Space Group	C 2 2 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 4	tiroidal mirror	2007-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	1.75	41.96	99.9	0.087	0.087	21.2	7.9	16926	16926			21.99

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	1.75	1.84	100		0.484	0.484	4.1	8	2441

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2H8V	1.75	30	15916	15916	992	99.89	0.16238	0.16238	0.16084	0.2038	0.18689	0.2314	RANDOM	11.954

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]
0.06			0.09		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.404
r_dihedral_angle_3_deg	12.752
r_dihedral_angle_4_deg	11.02
r_dihedral_angle_1_deg	5.404
r_scangle_it	2.839
r_scbond_it	1.835
r_angle_refined_deg	1.277
r_angle_other_deg	1.208
r_mcangle_it	1.141
r_mcbond_it	0.632

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.404
r_dihedral_angle_3_deg	12.752
r_dihedral_angle_4_deg	11.02
r_dihedral_angle_1_deg	5.404
r_scangle_it	2.839
r_scbond_it	1.835
r_angle_refined_deg	1.277
r_angle_other_deg	1.208
r_mcangle_it	1.141
r_mcbond_it	0.632
r_mcbond_other	0.194
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	907
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	44

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.