3BZD

Manipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.0 M ammonium sulfate, 0.1 M Tris-Cl pH 7.0, 0.3 % 1,6-diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.97	α = 90
b = 96.97	β = 90
c = 92.51	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2007-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.3	30	99.7	0.058			23532	21938	2	2	31.3

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)
	2.3	2.36	93.3		0.356			1518

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.3	27.99	21938	1073	100	0.213	0.21	0.258	RANDOM	18.38

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]
1.51	0.76		1.51		-2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.201
r_dihedral_angle_4_deg	19.678
r_dihedral_angle_3_deg	18.367
r_dihedral_angle_1_deg	5.887
r_scangle_it	4.76
r_scbond_it	3.911
r_mcangle_it	2.435
r_angle_refined_deg	2.359
r_mcbond_it	1.663
r_nbtor_refined	0.343

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.201
r_dihedral_angle_4_deg	19.678
r_dihedral_angle_3_deg	18.367
r_dihedral_angle_1_deg	5.887
r_scangle_it	4.76
r_scbond_it	3.911
r_mcangle_it	2.435
r_angle_refined_deg	2.359
r_mcbond_it	1.663
r_nbtor_refined	0.343
r_nbd_refined	0.326
r_symmetry_vdw_refined	0.299
r_xyhbond_nbd_refined	0.244
r_chiral_restr	0.158
r_symmetry_hbond_refined	0.123
r_bond_refined_d	0.031
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2755
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	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 R01GM133198.