1N7D | pdb_00001n7d

Extracellular domain of the LDL receptor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AJJ	PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5
experimental model	PDB	1D2J	PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5
experimental model	PDB	1I0U	PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5
experimental model	PDB	1IJQ	PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5
experimental model	PDB	1FX5	PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	298	acetate buffer pH 5.3, 1,2-hexanediol, 0.5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
5.43	77.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.29	α = 90
b = 185.29	β = 90
c = 85.186	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 4		2001-12-20	M	MAD
2	1		CCD	ADSC QUANTUM 210
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.21363, 1.21423, 1.10696, 1.23985	ALS	5.0.2
2	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1
3	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	3.7	45.3	95.6	0.09	9.8	3.7		17303			74.7

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	3.7	3.83	64.5		0.449	2.7

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5	3.7	45.3	17303	16008	1119	87.8	0.381	0.382	RANDOM	124.7

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]
20.49	9.97		20.49		-40.98

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.7
c_angle_deg	4.9
c_improper_angle_d	2.52
c_bond_d	0.031

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4702
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	254

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
CNS	refinement
CCP4	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.