3D74 | pdb_00003d74

Crystal structure of a pheromone binding protein mutant D35A, from Apis mellifera, soaked at pH 5.5

X-RAY DIFFRACTION

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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	5.5	293	2.1M ammonium sulfate, 0.2M di-ammonium phosphate, 20mM di-sodium phosphate, pH7.0, crystal was soaked in the same condition at pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.133	α = 90
b = 60.769	β = 90
c = 56.27	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	2008-01-21	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	2.1	30.39	99.8	0.066	0.066	14.5	3.9	12708	12708			24.26

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)
	2.1	2.21	100		0.29	0.29	4.3	3.8	1804

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	2.1	15	11717	11717	949	99.63	0.17886	0.17886	0.17472	0.22	0.22921	0.25	RANDOM	28.728

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]
2.61			-2.3		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.55
r_dihedral_angle_4_deg	19.016
r_dihedral_angle_3_deg	12.851
r_dihedral_angle_1_deg	9.154
r_scangle_it	2.509
r_scbond_it	2.048
r_angle_refined_deg	1.469
r_angle_other_deg	1.004
r_mcbond_it	0.881
r_mcangle_it	0.867
r_nbd_refined	0.233
r_nbd_other	0.2
r_symmetry_vdw_other	0.192
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.178
r_mcbond_other	0.158
r_chiral_restr	0.1
r_symmetry_vdw_refined	0.093
r_nbtor_other	0.089
r_bond_refined_d	0.012
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	1845
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	42

Software

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