2ISZ | pdb_00002isz

Crystal structure of a two-domain IdeR-DNA complex crystal form I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U8R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	28% PEG 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.832	α = 106.57
b = 69.739	β = 104.85
c = 76.461	γ = 99.66

Symmetry
Space Group	P 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 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0781	ALS	8.2.2

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	2.4	50	90.4	0.075	8.9			34892

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)
	2.4	2.49	60.7		0.296			2361

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1U8R	2.403	50	34889	1754	90.04	0.201	0.199	0.2	0.239	0.24	RANDOM	40.298

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]
0.75	0.55	0.48	-0.85	-1.45	-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.951
r_dihedral_angle_4_deg	19.238
r_dihedral_angle_3_deg	16.9
r_dihedral_angle_1_deg	4.65
r_mcangle_it	1.872
r_scangle_it	1.648
r_scbond_it	1.236
r_angle_refined_deg	1.134
r_mcbond_it	1.072
r_metal_ion_refined	0.32
r_nbtor_refined	0.315
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.216
r_symmetry_hbond_refined	0.208
r_symmetry_vdw_refined	0.201
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4440
Nucleic Acid Atoms	1347
Solvent Atoms	142
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection