3N5N | pdb_00003n5n

Crystal structure analysis of the catalytic domain and interdomain connector of human MutY homologue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MUY	PDB Entry 1MUY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	298	20% PEG 3350, 0.2M Magnesium acetate, 0.005 M tris[2-carboxyethyl] phosphine (TCEP), 5% glycerol, 0.01 M spermidine, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.311	α = 90
b = 82.167	β = 100.9
c = 63.46	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 210	Si(111) channel-cut monochromator, toroidal focusing mirror	2007-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.65	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	62.31	95.8	0.097	18.7	7.6	27002	25872

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.36	93.4		0.437	4.6	7.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD and Molecular Replacement	THROUGHOUT	PDB Entry 1MUY	2.3	62.31	27002	24674	1302	95.66	0.20843	0.20616	0.21	0.25078	0.25	RANDOM	64.249

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]
2.45		-2.6	-5.43		2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.257
r_dihedral_angle_3_deg	15.363
r_dihedral_angle_4_deg	15.092
r_scangle_it	9.115
r_scbond_it	6.328
r_dihedral_angle_1_deg	5.891
r_mcangle_it	3.835
r_mcbond_it	2.459
r_angle_refined_deg	1.991
r_chiral_restr	0.159
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4037
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	19

Software

Software
Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling