8BXU | pdb_00008bxu

Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with MPD (2-Methyl-2,4-pentanediol)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q8I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.12M Monosaccharides (0.02 M each of D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D-Glucosamine), 0.1 M Bicine/Trizma base, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350 and 12.5% (v/v) MPD (2-Methyl-2,4-pentanediol)

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.943	α = 90
b = 35.509	β = 100.49
c = 55.063	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 X 16M		2017-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	1.35	54.14	96.5	0.999	12.7	2.8		27461

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	1.35	1.42	95.9		0.749	2

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	1.35	33.398	27448	1393	96.076	0.167	0.1657	0.17	0.1941	0.2	21.07

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]
0.772		0.383	0.138		-0.985

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.656
r_dihedral_angle_4_deg	22.11
r_dihedral_angle_3_deg	12.967
r_dihedral_angle_1_deg	6.108
r_lrange_it	5.974
r_lrange_other	5.885
r_scangle_it	5.063
r_scangle_other	5.06
r_scbond_it	3.323
r_scbond_other	3.321
r_mcangle_it	2.594
r_mcangle_other	2.592
r_angle_refined_deg	1.89
r_mcbond_other	1.81
r_mcbond_it	1.809
r_angle_other_deg	1.563
r_symmetry_nbd_refined	0.293
r_nbd_refined	0.276
r_nbd_other	0.244
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.144
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.101
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.013
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	31

Software

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