2P71 | pdb_00002p71

Bombyx mori pheromone binding protein bound to iodohexadecane

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	PEG 4000, Tris, MgSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.79	α = 90
b = 83.79	β = 90
c = 34.88	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.95	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.006	59.76	92			13400	11314	2		26

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1DQE	2.006	59.76	8056	392	97.21	0.223	0.223	0.22	0.23	0.265	0.26	RANDOM	29.882

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]
-0.68			-0.68		1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.943
r_scangle_it	6.228
r_scbond_it	4.331
r_mcangle_it	3.109
r_angle_refined_deg	2.815
r_mcbond_it	1.863
r_angle_other_deg	1.334
r_symmetry_vdw_other	0.32
r_nbd_refined	0.293
r_nbd_other	0.256
r_xyhbond_nbd_refined	0.208
r_symmetry_vdw_refined	0.187
r_chiral_restr	0.181
r_symmetry_hbond_refined	0.129
r_nbtor_other	0.105
r_bond_refined_d	0.038
r_gen_planes_other	0.032
r_gen_planes_refined	0.021
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1038
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	17

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection