3D78 | pdb_00003d78

Dimeric crystal structure of a pheromone binding protein mutant D35N, from apis mellifera, at pH 7.0

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D73	PDB ENTRY 3D73

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
2.05	40.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.054	α = 90
b = 60.948	β = 90
c = 57.334	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	CCD	ADSC QUANTUM 315	Tiroidal mirror	2008-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.984	ESRF	ID23-2

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	1.55	50	99.6	0.048	0.048	20.3	4.4	32103	32103			18.48

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)
	1.55	1.63	99.6		0.321	0.321	3.8	4.2	4588

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3D73	1.6	15	28039	28039	1200	99.54	0.16088	0.16088	0.15897	0.21	0.20597	0.26	RANDOM	21.421

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]
1.17			-2.08		0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.605
r_dihedral_angle_4_deg	14.447
r_dihedral_angle_3_deg	11.01
r_dihedral_angle_1_deg	10.304
r_sphericity_free	6.128
r_scangle_it	3.187
r_scbond_it	2.546
r_sphericity_bonded	2.272
r_mcangle_it	1.562
r_angle_refined_deg	1.498
r_rigid_bond_restr	1.298
r_mcbond_it	1.261
r_angle_other_deg	0.985
r_mcbond_other	0.434
r_xyhbond_nbd_refined	0.271
r_symmetry_hbond_refined	0.244
r_nbd_refined	0.239
r_symmetry_vdw_other	0.236
r_symmetry_vdw_refined	0.209
r_nbd_other	0.204
r_nbtor_refined	0.183
r_nbtor_other	0.086
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1905
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	66

Software

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