3D73 | pdb_00003d73

Crystal structure of a pheromone binding protein mutant D35A, from Apis mellifera, at pH 7.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H8V	PDB ENTRY 2H8V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	2.1M ammonium sulfate, 0.2M di-ammonium phosphate, 20mM di-sodium phosphate, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.873	α = 90
b = 60.859	β = 90
c = 56.682	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	polar mirror	2008-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.01	30.43	97.4	0.057	0.057	22.2	6.2	14418	14418			21.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.01	2.12	82.2		0.254	0.254	6.4	5.9	10192

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 2H8V	2.03	20	13343	13343	1031	99.5	0.17535	0.17535	0.17166	0.21	0.22409	0.26	RANDOM	27.559

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]
1.13			-1.58		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.863
r_dihedral_angle_4_deg	22.622
r_dihedral_angle_3_deg	13.283
r_dihedral_angle_1_deg	9.444
r_scangle_it	2.781
r_scbond_it	1.989
r_angle_refined_deg	1.375
r_mcbond_it	1.078
r_mcangle_it	1.029
r_angle_other_deg	0.982
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.214
r_nbd_other	0.197
r_symmetry_hbond_refined	0.188
r_mcbond_other	0.186
r_symmetry_vdw_other	0.184
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.178
r_chiral_restr	0.095
r_nbtor_other	0.09
r_bond_refined_d	0.013
r_bond_other_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1846
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing