3CDN | pdb_00003cdn

Crystal structure of a pheromone binding protein from Apis mellifera soaked at pH 4.0

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	1.9M ammonium sulfate, 0.1M sodium citrate, pH5.5, crystal was soaked in the same condition at pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.146	α = 90
b = 83.53	β = 90
c = 47.361	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	CCD	ADSC QUANTUM 4r	Tiroidal mirror	2007-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	57.45	99.8	0.069	0.069	15.3	5	10923	10923			31.18

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	2	2.11	100		0.46	0.46	3.4	5	7880

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 3BJH	2	40	9844	9844	1075	99.64	0.17382	0.17382	0.17068	0.1833	0.20315	0.2204	RANDOM	65.231

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]
0.57			-0.36		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.899
r_dihedral_angle_3_deg	14.544
r_dihedral_angle_4_deg	10.633
r_dihedral_angle_1_deg	5.891
r_scangle_it	2.372
r_scbond_it	1.669
r_angle_refined_deg	1.3
r_mcangle_it	1.063
r_angle_other_deg	0.937
r_mcbond_it	0.888
r_symmetry_hbond_refined	0.342
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.209
r_mcbond_other	0.204
r_nbd_other	0.192
r_nbtor_refined	0.182
r_symmetry_vdw_other	0.176
r_nbtor_other	0.09
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	899
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	19

Software

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