6WN4 | pdb_00006wn4

Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D8J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	16-22% PEG 3350, 250mM Sodium Thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.624	α = 90
b = 67.745	β = 94.369
c = 130.073	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 EIGER X 9M	NULL	2019-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.74	29.264	99.29	0.12	0.133	0.057	0.995	10.4	5.1		23348

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.74	2.84	93.72		0.692	0.769	0.33	0.729	1.9	5.08

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5D8J	2.8	29.264	22291	1066	99.816	0.21	0.2079	0.22	0.2427	0.25	Random selection	54.434

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]
1.721		-2.888	2.905		-4.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.766
r_dihedral_angle_4_deg	16.247
r_dihedral_angle_3_deg	15.146
r_dihedral_angle_1_deg	6.917
r_lrange_it	4.519
r_lrange_other	4.519
r_mcangle_it	1.916
r_mcangle_other	1.916
r_scangle_it	1.531
r_scangle_other	1.531
r_angle_refined_deg	1.263
r_mcbond_it	1.076
r_mcbond_other	1.076
r_angle_other_deg	1.073
r_scbond_it	0.865
r_scbond_other	0.864
r_nbd_other	0.176
r_symmetry_nbd_other	0.165
r_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.161
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.153
r_symmetry_nbd_refined	0.143
r_ncsr_local_group_3	0.135
r_ncsr_local_group_2	0.122
r_ncsr_local_group_1	0.104
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.039
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6797
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing