3D77 | pdb_00003d77

Crystal structure of a pheromone binding protein mutant D35N, 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	3D75	PDB ENTRY 3D75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, crystal was soaked in the same condition at pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	58.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.215	α = 90
b = 83.999	β = 90
c = 47.54	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 315	Tiroidal mirror	2008-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.979	ESRF	ID29

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	1.7	57.64	99.1	0.047	0.047	26.4	6.8	17650	17650			24.53

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)
	1.7	1.79	99.6		0.349	0.349	4.5	7	2545

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	1.7	30	16595	16595	1044	98.96	0.16309	0.16309	0.16133	0.18	0.19131	0.2	RANDOM	24.694

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]
-0.63			0.44		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.677
r_dihedral_angle_3_deg	14.449
r_dihedral_angle_1_deg	13.982
r_sphericity_free	7.75
r_dihedral_angle_4_deg	7.465
r_rigid_bond_restr	3.941
r_scangle_it	3.928
r_sphericity_bonded	3.807
r_scbond_it	3.086
r_angle_refined_deg	2.211
r_mcangle_it	2.086
r_angle_other_deg	1.918
r_mcbond_it	1.346
r_mcbond_other	0.635
r_symmetry_vdw_refined	0.394
r_symmetry_hbond_refined	0.284
r_nbd_refined	0.269
r_symmetry_vdw_other	0.258
r_xyhbond_nbd_refined	0.232
r_nbd_other	0.207
r_nbtor_refined	0.192
r_chiral_restr	0.104
r_nbtor_other	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	947
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	39

Software

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