8C56 | pdb_00008c56

CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA

X-RAY DIFFRACTION

---

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
2.81	56.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.259	α = 90
b = 84.259	β = 90
c = 173.883	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		2013-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

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	2.4	20	99.6	0.114	0.121	0.999	16.89	8.6		25251			53.298

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	2.4	2.54	99		1.203	1.277	0.703	2.05	8.8

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	2.4	19.89	23997	1253	99.56	0.17535	0.17326	0.18	0.21625	0.22	RANDOM	51.84

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]
0.58			0.58		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.755
r_dihedral_angle_4_deg	14.394
r_dihedral_angle_3_deg	14.346
r_dihedral_angle_1_deg	5.523
r_long_range_B_refined	3.77
r_long_range_B_other	3.279
r_mcangle_it	1.187
r_mcangle_other	1.187
r_angle_refined_deg	1.006
r_scangle_other	0.951
r_angle_other_deg	0.795
r_mcbond_it	0.646
r_mcbond_other	0.643
r_scbond_it	0.52
r_scbond_other	0.52
r_chiral_restr	0.06
r_bond_refined_d	0.009
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	3199
Nucleic Acid Atoms	569
Solvent Atoms	412
Heterogen Atoms	33

Software

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