6PYC

Structure of kappa-on-heavy (KoH) antibody Fab bound to the cardiac hormone marinobufagenin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YHY	4YHY, 5DQD, 4LRN, 1EEQ, 4WCY
experimental model	PDB	5DQD	4YHY, 5DQD, 4LRN, 1EEQ, 4WCY
experimental model	PDB	4LRN	4YHY, 5DQD, 4LRN, 1EEQ, 4WCY
experimental model	PDB	1EEQ	4YHY, 5DQD, 4LRN, 1EEQ, 4WCY
experimental model	PDB	4WCY	4YHY, 5DQD, 4LRN, 1EEQ, 4WCY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M citric acid; 0.8 M ammonium sulfate; pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
3.74	67.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.483	α = 90
b = 128.483	β = 90
c = 333.335	γ = 90

Symmetry
Space Group	I 4 2 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 S 6M		2016-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9798	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.6	100	91.9	0.298	0.32	0.111	5.5	8.4		15341		-3

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	3.6	3.66	93.4		1.118	1.215	0.452	0.539		7.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4YHY, 5DQD, 4LRN, 1EEQ, 4WCY	3.6	47.44	14000	711	88.07	0.2364	0.2339	0.2871	RANDOM	92.198

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]
-1.63			-1.63		3.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.01
r_dihedral_angle_4_deg	17.707
r_dihedral_angle_3_deg	15.483
r_dihedral_angle_1_deg	7.671
r_angle_refined_deg	1.39
r_angle_other_deg	1.215
r_mcangle_it	1.09
r_mcbond_it	0.605
r_mcbond_other	0.605
r_chiral_restr	0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.01
r_dihedral_angle_4_deg	17.707
r_dihedral_angle_3_deg	15.483
r_dihedral_angle_1_deg	7.671
r_angle_refined_deg	1.39
r_angle_other_deg	1.215
r_mcangle_it	1.09
r_mcbond_it	0.605
r_mcbond_other	0.605
r_chiral_restr	0.06
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6475
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
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 R01GM133198.