3BFH

Crystal structure of a pheromone binding protein from Apis mellifera in complex with hexadecanoic acid

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R5R	PDB ENTRY 1R5R

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
3.06	59.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.26	α = 90
b = 84.348	β = 90
c = 47.666	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 210	toroidal mirror	2007-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	2	58.72	99.1	0.062	0.062	15.2	5	11157	11157			32.73

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	2	2.11	99.5		0.459	0.459	3.8	5.1	1604

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 1R5R	2	40	10190	10190	984	99.07	0.17609	0.17609	0.1726	0.19	0.21032	0.22	RANDOM	41.526

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]
0.73			0.39		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.753
r_dihedral_angle_3_deg	15.837
r_dihedral_angle_4_deg	10.319
r_dihedral_angle_1_deg	6.14
r_scangle_it	2.265
r_scbond_it	1.546
r_angle_refined_deg	1.41
r_angle_other_deg	1.057
r_mcangle_it	0.952
r_mcbond_it	0.696
r_symmetry_vdw_other	0.248
r_xyhbond_nbd_refined	0.232
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.217
r_symmetry_hbond_refined	0.214
r_mcbond_other	0.197
r_nbd_other	0.182
r_nbtor_refined	0.179
r_chiral_restr	0.114
r_nbtor_other	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	899
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	19

Software

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