2GYK | pdb_00002gyk

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.3	277	24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.903	α = 90
b = 88.248	β = 91.92
c = 52.235	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	CCD	ADSC QUANTUM 4		2000-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87	SRS	PX9.6

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	1.6	20	96.3	0.027	34.4		51260	51260	1	1

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)
	1.6	1.66	84.5		0.045			4468

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EMV	1.6	19.86	3	53245	51228	2598	96.21	0.187	0.187	0.185	0.2	0.232	0.24	RANDOM	15.426

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]
0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.306
r_dihedral_angle_4_deg	17.686
r_dihedral_angle_3_deg	13.353
r_dihedral_angle_1_deg	5.806
r_scangle_it	3.309
r_scbond_it	2.149
r_mcangle_it	1.248
r_angle_refined_deg	1.229
r_mcbond_it	0.805
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.306
r_dihedral_angle_4_deg	17.686
r_dihedral_angle_3_deg	13.353
r_dihedral_angle_1_deg	5.806
r_scangle_it	3.309
r_scbond_it	2.149
r_mcangle_it	1.248
r_angle_refined_deg	1.229
r_mcbond_it	0.805
r_nbtor_refined	0.297
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.146
r_metal_ion_refined	0.113
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3373
Nucleic Acid Atoms
Solvent Atoms	686
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
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.