4RUN | pdb_00004run

Crystal structure of human odorant binding protein OBPIIa

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	Protein solution: 14 mg/ml protein, 0.2 M imidazole, 0.4 M NaCl, 10 mM Tris-HCl, 1.3 mM Menthol, 3.3 %(v/v) Methanol; Reservoir solution: 20 %(w/v) PEG 3350, 0.1 M ammonium citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.949	α = 90
b = 52.949	β = 90
c = 232.098	γ = 90

Symmetry
Space Group	P 41 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	CCD	MARMOSAIC 225 mm CCD	MIRRORS	2011-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	2.6	35	99.7	0.049	31.88	8.8	10926	10926	-3	-3	63.91

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	2.6	2.7	97.5		0.645	2.76

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	MOLECULAR REPLACEMENT	THROUGHOUT	3EYC	2.6	33.7	10926	10926	523	99.64	0.2373	0.2373	0.235	0.24	0.2844	0.29	RANDOM	75.6

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]
-0.92			-0.92		1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.553
r_dihedral_angle_4_deg	20.701
r_dihedral_angle_3_deg	15.354
r_dihedral_angle_1_deg	6.52
r_mcangle_it	3.74
r_mcbond_it	2.16
r_mcbond_other	2.16
r_angle_refined_deg	1.309
r_angle_other_deg	0.908
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2405
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
PHASER	phasing