3GJN | pdb_00003gjn

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FR2	PDB ENTRY 1FR2, 1ZNV
experimental model	PDB	1ZNV	PDB ENTRY 1FR2, 1ZNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		10.5	292	30% PEG40, pH10.5, Microbatch under oil, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.65	α = 90
b = 53.713	β = 105.59
c = 79.334	γ = 90

Symmetry
Space Group	P 1 21 1

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++	mirrors	2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.15	50	94.2	0.154	0.143	8.63	3.4		15983			39.86

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	83.9		0.327	0.276	2.3	2.5	1405

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FR2, 1ZNV	2.48	43.94	16503	15160	814	91.86	0.24403	0.24233	0.248	0.27566	0.2765	RANDOM	39.864

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]
-1.45		-3.75	-4.03		3.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.565
r_dihedral_angle_4_deg	25.248
r_dihedral_angle_3_deg	22.061
r_dihedral_angle_1_deg	9.271
r_scangle_it	5.236
r_scbond_it	3.548
r_angle_refined_deg	2.511
r_mcangle_it	2.089
r_mcbond_it	1.51
r_symmetry_vdw_refined	0.359
r_nbtor_refined	0.325
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.219
r_chiral_restr	0.177
r_symmetry_hbond_refined	0.175
r_metal_ion_refined	0.099
r_bond_refined_d	0.028
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3226
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling