3DSC | pdb_00003dsc

Crystal structure of P. furiosus Mre11 DNA synaptic complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1II7	PDB ENTRY 1II7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20% PEG 1000, 0.1 M Tris-HCl, 0.2 M MgCl2, 0.2 M 1,6 hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.477	α = 90
b = 106.071	β = 90
c = 76.667	γ = 90

Symmetry
Space Group	C 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2		ALS	5.0.2

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	2.7	20	94.5	0.085	17.6	4.8		10769	1	1

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 (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 1II7	2.7	19.94	10769	9708	545	95.55	0.23034	0.23034	0.22756	0.23	0.27804	0.27	RANDOM	42.368

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]
-1.71			4.77		-3.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.481
r_dihedral_angle_4_deg	16.295
r_dihedral_angle_3_deg	16.059
r_dihedral_angle_1_deg	4.865
r_angle_refined_deg	0.983
r_mcangle_it	0.354
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.238
r_mcbond_it	0.199
r_xyhbond_nbd_refined	0.152
r_nbd_refined	0.146
r_symmetry_vdw_refined	0.129
r_scangle_it	0.099
r_chiral_restr	0.072
r_scbond_it	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2754
Nucleic Acid Atoms	348
Solvent Atoms	63
Heterogen Atoms

Software

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