3DW9 | pdb_00003dw9

SgrAI with cognate DNA and manganese bound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			PEG4000, buffer, NaCl, MnCl2, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.261	α = 90
b = 117.101	β = 112.96
c = 63.702	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

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	2.2		88.6	0.074	16	3.4		35508

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	2.2	58.62	33752	1756	88.6	0.17678	0.17351	0.18	0.23957	0.24	RANDOM	39.131

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]
-0.89		2.14	-2.29		4.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.664
r_dihedral_angle_3_deg	16.752
r_dihedral_angle_4_deg	16.219
r_dihedral_angle_1_deg	7.29
r_scangle_it	3.54
r_scbond_it	2.305
r_angle_refined_deg	1.946
r_mcangle_it	1.581
r_angle_other_deg	1.04
r_mcbond_it	0.881
r_mcbond_other	0.182
r_chiral_restr	0.108
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5280
Nucleic Acid Atoms	732
Solvent Atoms	319
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling