7R8U | pdb_00007r8u

LOX-1 - Structural and Functional Studies of a Receptor Implicated in Atherosclerosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YPU	PDB entry 1YPU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1 M Tris base, BICINE, pH 8.5, 50% v/v precipitant mix (25% v/v MPD, 25% PEG1000, 25% w/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.908	α = 90
b = 89.901	β = 90
c = 110.925	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 325 mm CCD		2019-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.19499	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.9	39.492	96.9	0.995	1.6	6.5		57364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			0.65

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YPU	1.901	39.492	56992	1175	99.509	0.187	0.1861	0.19	0.2181	0.23	36.913

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]
-0.083			-2.628		2.711

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.568
r_dihedral_angle_4_deg	17.46
r_dihedral_angle_3_deg	15.624
r_dihedral_angle_1_deg	7.372
r_lrange_it	7.363
r_lrange_other	7.362
r_scangle_it	5.713
r_scangle_other	5.713
r_mcangle_it	4.395
r_mcangle_other	4.394
r_scbond_it	3.914
r_scbond_other	3.913
r_mcbond_it	3.187
r_mcbond_other	3.186
r_angle_refined_deg	1.611
r_angle_other_deg	1.341
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_other	0.227
r_symmetry_nbd_refined	0.217
r_nbd_refined	0.202
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.161
r_ncsr_local_group_1	0.136
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.077
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5407
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing