2FJY

Crystal Structure of B-form Bombyx mori Pheromone Binding Protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GM0	pdb entry 1GM0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	NaF, PEG 3350, pH 7.5, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.24	α = 90
b = 70.79	β = 90
c = 75.49	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		CCD			2002-06-05		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.950	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	43	91				12094	2	2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1GM0	2.3	43	13439	12080	605	89.89	0.222	0.22	0.22	0.27	RANDOM	26.569

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]
-0.23			2.59		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.05
r_dihedral_angle_1_deg	5.562
r_scbond_it	5.153
r_mcangle_it	4.414
r_angle_refined_deg	2.533
r_mcbond_it	2.324
r_angle_other_deg	1.133
r_symmetry_vdw_other	0.365
r_symmetry_vdw_refined	0.314
r_nbd_other	0.25
r_nbd_refined	0.231
r_symmetry_hbond_refined	0.216
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.174
r_nbtor_other	0.098
r_bond_refined_d	0.048
r_gen_planes_refined	0.015
r_gen_planes_other	0.013
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2166
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms

Software

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