3BYY | pdb_00003byy

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
3.17	61.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.69	α = 90
b = 96.69	β = 90
c = 91.84	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	CCD	ADSC QUANTUM 4		2006-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	0.9902	NSLS	X12B

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	50	97.6	0.059			33391	27415	2	2	33.9

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	2.2	50	24792	1287	99.95	0.192	0.19	0.19	0.233	0.23	RANDOM	32.846

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]
1.25	0.62		1.25		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.044
r_dihedral_angle_3_deg	15.317
r_dihedral_angle_4_deg	10.075
r_dihedral_angle_1_deg	6.491
r_scangle_it	5.064
r_scbond_it	3.454
r_mcangle_it	2.291
r_angle_refined_deg	1.739
r_mcbond_it	1.421
r_symmetry_hbond_refined	0.347

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.044
r_dihedral_angle_3_deg	15.317
r_dihedral_angle_4_deg	10.075
r_dihedral_angle_1_deg	6.491
r_scangle_it	5.064
r_scbond_it	3.454
r_mcangle_it	2.291
r_angle_refined_deg	1.739
r_mcbond_it	1.421
r_symmetry_hbond_refined	0.347
r_nbtor_refined	0.305
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.115
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2752
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	10

Software

Software
Software Name	Purpose
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.