3BVG | pdb_00003bvg

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M Tris-Cl, pH 8.5, 2.4 M ammonium sulfate, 2.25% polyethylene glycol (PEG) 400 and 2.25% Tween 20, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 42.7	β = 90
c = 287.142	γ = 90

Symmetry
Space Group	P 43 21 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	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic mirrors	2004-06-30	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	50	86	0.063				16498	2	2	26.5

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 (All)	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	30	16493	844	85.82	0.225	0.216	0.213	0.2109	0.276	0.271	RANDOM	16.47

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			0.09		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.873
r_dihedral_angle_4_deg	21.016
r_dihedral_angle_3_deg	15.053
r_dihedral_angle_1_deg	7.099
r_scangle_it	4.208
r_scbond_it	2.91
r_mcangle_it	1.944
r_angle_refined_deg	1.755
r_mcbond_it	1.225
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.263
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.198
r_symmetry_hbond_refined	0.171
r_chiral_restr	0.128
r_symmetry_metal_ion_refined	0.067
r_metal_ion_refined	0.047
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1866
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing