3SSD | pdb_00003ssd

DNA binding domain of restriction endonuclease bound to DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop	6.8	292	0.2 M LiCl, 18% PEG4000, pH 6.8, sitting drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.75	35.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.085	α = 90
b = 67.189	β = 90
c = 142.414	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	FLAT PANEL	MAR555		2008-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81500	EMBL/DESY, HAMBURG	X11

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	2.2	29.03	99.8	0.07	0.07	18.8	5.6		18339

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)
1	2.2	2.32	99.9		0.254	0.254	1.2	5.3

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	MR	THROUGHOUT	2.2	19.02	16474	16474	1794	99.51	0.20199	0.1955	0.1929	0.26221	0.2566	RANDOM	42.829

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]
-2.57			2.83		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.984
r_dihedral_angle_4_deg	24.19
r_dihedral_angle_3_deg	16.067
r_dihedral_angle_1_deg	6.62
r_scangle_it	3.23
r_scbond_it	2.473
r_mcangle_it	1.826
r_angle_refined_deg	1.353
r_mcbond_it	1.144
r_nbtor_refined	0.287
r_nbd_refined	0.143
r_symmetry_vdw_refined	0.112
r_chiral_restr	0.088
r_xyhbond_nbd_refined	0.083
r_symmetry_hbond_refined	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
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	2483
Nucleic Acid Atoms	487
Solvent Atoms	136
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing