2C7O | pdb_00002c7o

HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MHT	PDB ENTRY 3MHT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE, 5 % GLUCOSE.

Crystal Properties
Matthews coefficient	Solvent content
2.74	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.18	α = 90
b = 95.18	β = 90
c = 312.547	γ = 120

Symmetry
Space Group	H 3 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	IMAGE PLATE	MARRESEARCH	MIRRORS	2004-03-18	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	23.2	99.6	0.05	11.4	21.6		43361		3.9	10.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	98.5		0.2	3.9	20.8

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3MHT	1.9	23.08	43361	4391	99.3	0.194	0.194	0.215	RANDOM	18.8

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]
1.11	0.91		1.11		-2.23

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.9
c_angle_deg	1.3
c_improper_angle_d	1.08
c_scangle_it	0.99
c_mcangle_it	0.78
c_scbond_it	0.57
c_mcbond_it	0.45
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2595
Nucleic Acid Atoms	509
Solvent Atoms	341
Heterogen Atoms	46

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing