3N7B | pdb_00003n7b

SgrAI bound to secondary site DNA and Ca(II)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	25 to 21% PEG 4K, 0.1 M HEPES buffer, 0.15-0.20 M NaCl, 0.05 M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.682	α = 90
b = 133.662	β = 90
c = 64.748	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	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2008-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	2.65	84.324	99.9	0.119	0.119	10.1	4.3	28125	28125	4	4

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)
	2.65	2.72	100		0.383	0.383	2	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.65	84.32	28132	26722	1362	100	0.17617	0.17255	0.18	0.24776	0.25	RANDOM	28.252

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]
-1.93			-0.08		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.153
r_dihedral_angle_3_deg	17.356
r_dihedral_angle_4_deg	13.887
r_dihedral_angle_1_deg	7.223
r_scangle_it	2.855
r_scbond_it	1.748
r_angle_refined_deg	1.683
r_mcangle_it	1.297
r_angle_other_deg	1.002
r_mcbond_it	0.683
r_mcbond_other	0.114
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5264
Nucleic Acid Atoms	650
Solvent Atoms	395
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHASER	phasing
MOSFLM	data reduction