3ZQ3 | pdb_00003zq3

Crystal Structure of Rat Odorant Binding Protein 3 (OBP3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A2U	PDB ENTRY 2A2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.02 M D-GLUCOSE, 0.02 M D-GALACTOSE, 0.02 M L-FUCOSE, 0.02M D-XYLOSE, 0.02M N-ACETYL-D-GLUCOSAMINE, 0.1 M MORPHEUS BUFFER 1 PH 6.5, 10 % W/V POLYETHYLENE GLYCOL, 20 % POLYETHYLENE GLYCOL 550

Crystal Properties
Matthews coefficient	Solvent content
2.64	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.98	α = 90
b = 100.53	β = 110.61
c = 72.41	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2012-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8	67.8	95.7	0.13	4.8	1.8		19952			48.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	95.1		0.48	1.8	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2A2U	2.8	67.776	19938	1025	95.279	0.219	0.2176	0.22	0.249	0.25	RANDOM	43.566

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]
-2.367		0.698	-0.107		1.723

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.412
r_dihedral_angle_4_deg	14.817
r_dihedral_angle_3_deg	14.636
r_dihedral_angle_1_deg	6.423
r_scangle_it	6.185
r_mcangle_it	5.343
r_scbond_it	3.775
r_mcbond_it	3.207
r_mcbond_other	3.207
r_angle_refined_deg	1.371
r_angle_other_deg	0.905
r_nbd_other	0.358
r_nbd_refined	0.197
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.123
r_xyhbond_nbd_other	0.107
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.005
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5132
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MrBUMP	phasing