1NGN | pdb_00001ngn

Mismatch repair in methylated DNA. Structure of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.26	289	PEG 2000 monomethyl ether, ammonium sulfate, ethylene glycol, sodium citrate, pH 5.26, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.58	α = 90
b = 48.58	β = 90
c = 146.57	γ = 120

Symmetry
Space Group	P 31 2 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	IMAGE PLATE	RIGAKU RAXIS IV		2000-10-16	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	BRANDEIS - B2		2000-11-05	M	MAD
3	1	x-ray	100	CCD	ADSC QUANTUM 4		2001-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418
2	SYNCHROTRON	NSLS BEAMLINE X12C	0.9789, 0.97865, 0.95	NSLS	X12C
3	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

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
1,2,3	2.1	20	99.5	0.046	42.7	8.73	12345	12345		-3	22.9

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)
	2.1	2.14	99.8		0.098			585

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	19.33	2	11028	11028	894	99.5	0.213	0.263	RANDOM	26.8

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]
2.09	1.87		2.09		-4.18

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	24.2
x_angle_d	1.4
x_improper_angle_d	0.65
x_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1214
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
X-PLOR	refinement