2B2V

Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B2T	WITHOUT CHAIN D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	283	4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
2.4	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.255	α = 90
b = 54.177	β = 111.97
c = 99.96	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARRESEARCH		2005-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	2.5	30.9	94.8	0.085	16.3	3.6		18233

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)
1	2.5	2.59	71.7		0.485	1.35	2.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY B2T WITHOUT CHAIN D	2.65	30.9	18233	16146	789	98.1	0.216	0.213	0.266	RANDOM	48.77

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]
-6.68		-2.7	6.29		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.948
r_dihedral_angle_4_deg	24.459
r_dihedral_angle_3_deg	22.463
r_dihedral_angle_1_deg	8.686
r_scangle_it	7.51
r_scbond_it	5.574
r_mcangle_it	3.56
r_mcbond_it	2.636
r_angle_refined_deg	1.709
r_angle_other_deg	1.107
r_mcbond_other	0.702
r_symmetry_vdw_other	0.566
r_symmetry_vdw_refined	0.53
r_chiral_restr	0.332
r_nbd_refined	0.33
r_nbd_other	0.303
r_symmetry_hbond_refined	0.284
r_nbtor_refined	0.223
r_xyhbond_nbd_refined	0.215
r_xyhbond_nbd_other	0.13
r_nbtor_other	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3556
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data scaling
MOLREP	phasing