6QM2 | pdb_00006qm2

NlaIV restriction endonuclease

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	294	10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'-CAGGTACCATG-3' strands. The protein-DNA solutions were in turn mixed in 1:1 ratio with the precipitant solution containing 2 M NaCl and 100 mM citric acid, pH 5.

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.38	α = 90
b = 110.38	β = 90
c = 209.006	γ = 120

Symmetry
Space Group	P 62 2 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	MARRESEARCH	BENT MIRROR	2008-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	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	2.8	30	98.5	0.043	0.04	28.92	7.5		18997

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	2.8	2.97	98.6		1.052	0.986	1.72	7.7

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	MAD	THROUGHOUT	2.8	29.72	18083	912	98.46	0.19245	0.19095	0.2	0.22103	0.22	RANDOM	115.889

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]
1.68	0.84		1.68		-5.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.834
r_dihedral_angle_4_deg	16.289
r_dihedral_angle_3_deg	13.639
r_long_range_B_refined	9.963
r_long_range_B_other	9.927
r_scangle_other	6.542
r_mcangle_it	6.427
r_mcangle_other	6.427
r_dihedral_angle_1_deg	5.289
r_mcbond_it	3.825
r_mcbond_other	3.814
r_scbond_it	3.765
r_scbond_other	3.765
r_angle_refined_deg	1.083
r_angle_other_deg	0.849
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2056
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
STARANISO	data scaling
autoSHARP	phasing
SHELXDE	phasing
SOLOMON	phasing
DM	phasing
PARROT	phasing
ARP/wARP	model building
BUCCANEER	model building