3HM5 | pdb_00003hm5

SANT domain of human DNA methyltransferase 1 associated protein 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	20% PEG3350, 0.2M calcium chloride, 0.1M HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.523	α = 90
b = 36.523	β = 90
c = 230.506	γ = 120

Symmetry
Space Group	P 61 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	IMAGE PLATE	MAR scanner 300 mm plate		2009-04-06	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate		2009-05-17	M	SINGLE WAVELENGTH
3	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate		2009-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.91987	APS	23-ID-B
2	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.07221	CLSI	08ID-1
3	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.00645	CLSI	08ID-1

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	1.8	40	96.8	0.079	44.467	17		9198

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)
	1.8	1.86	75.6		0.47		6.2	693

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	SIRAS	THROUGHOUT	1.8	19.905	9080	433	97.04	0.225	0.223	0.23	0.275	0.29	RANDOM	17.685

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]
0.121	0.06		0.121		-0.181

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.836
r_dihedral_angle_4_deg	17.197
r_dihedral_angle_3_deg	11.336
r_dihedral_angle_1_deg	6.521
r_scangle_it	4.439
r_scbond_it	2.762
r_mcangle_it	1.927
r_angle_refined_deg	1.455
r_mcbond_it	1.08
r_angle_other_deg	0.96
r_mcbond_other	0.302
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	644
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling