3E8U | pdb_00003e8u

Crystal structure and thermodynamic analysis of diagnostic Fab 106.3 complexed with BNP 5-13 (C10A) reveal basis of selective molecular recognition

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.9	α = 90
b = 88.878	β = 90
c = 138.509	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	1.0	APS	17-BM

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	2.1	50	90.3	0.089		5.3		25672

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)
	2.1	2.18	53.7		0.356		2	1508

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.1	44.73	25645	1314	90.29	0.188	0.185	0.19	0.243	0.24	RANDOM	20.195

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]
-0.09			-0.16		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.456
r_dihedral_angle_4_deg	18.327
r_dihedral_angle_3_deg	13.827
r_dihedral_angle_1_deg	6.513
r_scangle_it	2.289
r_scbond_it	1.429
r_angle_refined_deg	1.236
r_mcangle_it	0.983
r_mcbond_it	0.558
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.456
r_dihedral_angle_4_deg	18.327
r_dihedral_angle_3_deg	13.827
r_dihedral_angle_1_deg	6.513
r_scangle_it	2.289
r_scbond_it	1.429
r_angle_refined_deg	1.236
r_mcangle_it	0.983
r_mcbond_it	0.558
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.262
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.184
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3366
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.