6PYC

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

X-RAY DIFFRACTION

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.