3D76 | pdb_00003d76

Crystal structure of a pheromone binding protein mutant D35N, from Apis mellifera, soaked 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	3D75	PDB ENTRY 3D75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, crystal was soaked in the same condition at pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	58.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.991	α = 90
b = 84.196	β = 90
c = 47.558	γ = 90

Symmetry
Space Group	C 2 2 21

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	2008-01-22	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	1.9	25.13	99.8	0.056	0.056	24.8	6.1	12833	12833			22.88

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)
	1.9	2	100		0.322	0.322	6.5	6	1837

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 3D75	1.9	15	11728	11728	947	98.85	0.19423	0.19423	0.19044	0.23	0.24146	0.28	RANDOM	26.522

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]
-0.55			-0.56		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.675
r_dihedral_angle_3_deg	14.019
r_dihedral_angle_4_deg	12.491
r_dihedral_angle_1_deg	6.516
r_scangle_it	2.572
r_angle_refined_deg	1.848
r_scbond_it	1.638
r_angle_other_deg	1.276
r_mcangle_it	1.05
r_mcbond_it	0.626
r_chiral_restr	0.29
r_symmetry_hbond_refined	0.264
r_symmetry_vdw_refined	0.263
r_xyhbond_nbd_refined	0.237
r_nbd_refined	0.231
r_nbd_other	0.209
r_nbtor_refined	0.185
r_symmetry_vdw_other	0.181
r_mcbond_other	0.162
r_nbtor_other	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	910
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	39

Software

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