8BXV | pdb_00008bxv

Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Thymol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BXU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.241	α = 90
b = 36.566	β = 100.383
c = 54.962	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 9M		2019-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.3	54.06	94.3	0.999	22.5	6.4		31153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.37	97.8		0.98		6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.3	54.06	31140	1581	93.948	0.187	0.1851	0.19	0.2202	0.23	22.994

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]
-0.221		0.265	0.89		-0.719

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.476
r_dihedral_angle_4_deg	16.419
r_dihedral_angle_3_deg	14.105
r_dihedral_angle_1_deg	6.396
r_lrange_it	6.097
r_lrange_other	6.006
r_scangle_it	4.349
r_scangle_other	4.347
r_scbond_it	2.996
r_scbond_other	2.994
r_mcangle_it	2.601
r_mcangle_other	2.6
r_angle_refined_deg	1.958
r_mcbond_other	1.807
r_mcbond_it	1.803
r_angle_other_deg	1.541
r_nbd_refined	0.295
r_nbd_other	0.2
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.121
r_metal_ion_refined	0.12
r_symmetry_nbd_refined	0.108
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	973
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing