6SUA | pdb_00006sua

Structure of the high affinity engineered lipocalin C1B12 in complex with the mouse CD98 heavy chain ectodomain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I9Q	6I9Q, 6S8V
experimental model	PDB	6S8V	6I9Q, 6S8V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	12 %(w/v) PEG8000, 0.2 M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.039	α = 90
b = 107.737	β = 90
c = 133.872	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS3 2M		2018-03-22	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)	Rrim I (All)	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	2.75	34.71	99.1	0.197	0.205	0.996	15.36	13.198		39856			42.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.85	96.6		1.079	1.128	0.769	2.45	11.718

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	6I9Q, 6S8V	2.75	34.71	37895	1961	99.09	0.2222	0.2197	0.22	0.2709	0.27	RANDOM	43.758

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]
-0.85			-3.22		4.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.391
r_dihedral_angle_4_deg	14.819
r_dihedral_angle_3_deg	14.552
r_dihedral_angle_1_deg	6.297
r_angle_refined_deg	1.182
r_angle_other_deg	1.068
r_chiral_restr	0.039
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.391
r_dihedral_angle_4_deg	14.819
r_dihedral_angle_3_deg	14.552
r_dihedral_angle_1_deg	6.297
r_angle_refined_deg	1.182
r_angle_other_deg	1.068
r_chiral_restr	0.039
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9424
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	60

Software

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

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.