8C57 | pdb_00008c57

CpG specific M.MpeI methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhaC) and 5-methylcytosine containing dsDNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DKJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	294	10% PEG 3350, 150 mM NaCl, 50 mM sodium citrate (final pH, 5.6). For cryoprotection glycerol was added to 25% v/v

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.453	α = 90
b = 84.453	β = 90
c = 172.565	γ = 90

Symmetry
Space Group	P 41 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	PIXEL	DECTRIS PILATUS 6M-F		2013-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.27820	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	CC (Half)	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	1.95	20	95	0.037	0.043	0.999	18.27	3.66		44130			48.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.07	96		0.701	0.822	0.685	1.8	3.58

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4DKJ	1.95	19.93	41915	2204	95.11	0.16317	0.16167	0.17	0.19202	0.2	RANDOM	48.612

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]
0.26			0.26		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.933
r_dihedral_angle_4_deg	15.159
r_dihedral_angle_3_deg	13.564
r_dihedral_angle_1_deg	5.381
r_long_range_B_refined	5.275
r_long_range_B_other	4.598
r_scangle_other	1.588
r_mcangle_it	1.339
r_mcangle_other	1.339
r_angle_refined_deg	1.091
r_scbond_it	0.917
r_scbond_other	0.916
r_angle_other_deg	0.842
r_mcbond_it	0.786
r_mcbond_other	0.786
r_chiral_restr	0.069
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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	3090
Nucleic Acid Atoms	570
Solvent Atoms	464
Heterogen Atoms	73

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
REFMAC	phasing
ARP/wARP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction