3MWY | pdb_00003mwy

Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H1E	PDB ENTRIES 2H1E,1Z63,1Z3I
experimental model	PDB	1Z63	PDB ENTRIES 2H1E,1Z63,1Z3I
experimental model	PDB	1Z3I	PDB ENTRIES 2H1E,1Z63,1Z3I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	18% PEG 3350; 400 mM K+/Na+ tartrate; 5% xylitol; 10 mM MgCl2; 1 mM ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.333	α = 90
b = 94.333	β = 90
c = 450.088	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	CCD	ADSC QUANTUM 315		2008-03-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9792,0.9611	NSLS	X29A

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	3.7	50	99.9	0.069	20.9	5.5	24026	20114	1	1

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	3.7	3.83	99.8		0.402	4.5	5.5

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	MAD	THROUGHOUT	PDB ENTRIES 2H1E,1Z63,1Z3I	3.7	50	12949	12949	688	99.94	0.26462	0.26186	0.26	0.31772	0.32	RANDOM	126.878

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]
3.44	1.72		3.44		-5.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.411
r_dihedral_angle_3_deg	24.559
r_dihedral_angle_4_deg	20.41
r_dihedral_angle_1_deg	8.405
r_angle_refined_deg	1.628
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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	5712
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
SOLVE	phasing
SHARP	phasing
PHENIX	refinement
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling