3CMX | pdb_00003cmx

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		RecA5 fusion protein was incubated with a 3-fold molar excess of ssDNA in the original protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6.0. Crystals of the RecA5-(ADP-AlF4-Mg)5-(dT)15 complex were grown from 50 mM Tris-Cl, 9% (w/v) PVP K15, 32% (v/v) MPD, 10 mM DTT, pH 8.0. RecA5-(ADP-AlF4-Mg)5-(dT)15-(dA)12 complex were obtained by soaking the RecA5-(ADP-AlF4-Mg)5-(dT)15 crystals in a 0.2 mM solution of the complementary (dA)12 oligonucleotide in 25 mM Tris-Cl, 9% (w/v) PVP K15, 32% (v/v) MPD, 2 mM ADP, 8 mM AlF4, and 10 mM MgCl2 for 4 hr.

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159	α = 90
b = 300.5	β = 90
c = 80.1	γ = 90

Symmetry
Space Group	P 21 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					2007-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C		APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.4	40					49365

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 (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	3.4	40	49365	1588	94.7	0.239	0.238	0.28	0.256	0.29	RANDOM	31.61

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]
-0.14			0.1		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.905
r_dihedral_angle_3_deg	19.105
r_dihedral_angle_4_deg	16.131
r_dihedral_angle_1_deg	5.083
r_scangle_it	2.422
r_scbond_it	1.499
r_mcangle_it	1.485
r_angle_refined_deg	1.186
r_mcbond_it	0.843
r_symmetry_vdw_refined	0.388
r_symmetry_hbond_refined	0.361
r_nbtor_refined	0.307
r_nbd_refined	0.205
r_metal_ion_refined	0.155
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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_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	24166
Nucleic Acid Atoms	963
Solvent Atoms
Heterogen Atoms	330

Software

Software
Software Name	Purpose
REFMAC	refinement