3S0B | pdb_00003s0b

Apis mellifera OBP14 in complex with the fluorescent probe 1-N-phenylnaphthylamine (NPN)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S0A	PDB ENTRY 3S0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.8	293	1.8-1.9 M tri-sodium citrate, 25 mM CHES, pH 9.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.38	α = 90
b = 37.11	β = 90
c = 89.75	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 315r	mirrors	2011-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1		SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.22	45	99.4	0.044	18	4.6	32858	32858			12

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	1.22	1.25	99		0.6	2.2	3.7	2387

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 3S0A	1.22	44.88	31192	31192	1666	99.43	0.16783	0.16783	0.16697	0.19	0.18347	0.21	RANDOM	8.081

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]
-0.05			-0.02		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.59
r_dihedral_angle_3_deg	11.645
r_dihedral_angle_4_deg	8.165
r_dihedral_angle_1_deg	5.311
r_scangle_it	4.561
r_scbond_it	2.903
r_mcangle_it	1.99
r_angle_refined_deg	1.513
r_rigid_bond_restr	1.309
r_mcbond_it	1.197

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.59
r_dihedral_angle_3_deg	11.645
r_dihedral_angle_4_deg	8.165
r_dihedral_angle_1_deg	5.311
r_scangle_it	4.561
r_scbond_it	2.903
r_mcangle_it	1.99
r_angle_refined_deg	1.513
r_rigid_bond_restr	1.309
r_mcbond_it	1.197
r_angle_other_deg	1.001
r_mcbond_other	0.479
r_chiral_restr	0.117
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	943
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	17

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.