3NDH

Restriction endonuclease in complex with substrate DNA

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	294	0.1M sodium acetate PH 4.5, 200MM, ammonium sulfate, 30% PEG400, 1.5% 1,2,3-heptanetriol, VAPOR, DIFFUSION, SITTING DROP, TEMPERATURE 294K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.31	α = 90
b = 72.91	β = 101.99
c = 88.76	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	100	CCD	MARRESEARCH	BENT MIRROR	2008-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	0.976	MPG/DESY, HAMBURG	BW6

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	1.3	20	98.7	0.074	0.074	5	2.8	118539	118539			14.24

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)
	1.3	1.37	99.4		0.266	0.266	2.8	2.2	17399

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	1.3	19.51	118512	118512	5962	98.61	0.1723	0.1723	0.17173	0.18318	RANDOM	19.942

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]
-1.49		-0.61	1.79		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.427
r_dihedral_angle_4_deg	18.648
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_1_deg	5.897
r_angle_other_deg	3.806
r_scangle_it	2.302
r_scbond_it	1.56
r_angle_refined_deg	1.261
r_mcangle_it	1.131
r_mcbond_it	0.627
r_symmetry_vdw_refined	0.267
r_nbd_other	0.245
r_nbd_refined	0.218
r_symmetry_vdw_other	0.211
r_nbtor_refined	0.191
r_symmetry_hbond_refined	0.155
r_metal_ion_refined	0.126
r_xyhbond_nbd_refined	0.118
r_nbtor_other	0.104
r_chiral_restr	0.08
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.008
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_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	3478
Nucleic Acid Atoms	404
Solvent Atoms	470
Heterogen Atoms	57

Software

Software
Software Name	Purpose
MAR345	data collection
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
SHARP	phasing
ARP/wARP	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling