3IIF

Crystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form B)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IID	PDB entry 3IID

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	294	0.8 M (NH4)2SO4, 0.2 M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.61	α = 90
b = 129.61	β = 90
c = 128.29	γ = 120

Symmetry
Space Group	H 3

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 315r		2006-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

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	2.1	64.82	99.7	0.074	14	5.1	46730	46730	-3		37

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	2.1	2.16	96.2		0.482	3.2	4.1	3651

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 3IID	2.1	64.82	44389	2337	100	0.1813	0.18005	0.20459	RANDOM	29.855

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]
0.06	0.03		0.06		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.768
r_dihedral_angle_4_deg	20.638
r_dihedral_angle_3_deg	17.558
r_dihedral_angle_1_deg	8.018
r_scangle_it	2.883
r_scbond_it	1.952
r_angle_refined_deg	1.662
r_mcangle_it	1.068
r_angle_other_deg	1.021
r_mcbond_it	0.84
r_nbd_refined	0.212
r_symmetry_vdw_other	0.204
r_symmetry_hbond_refined	0.192
r_nbd_other	0.185
r_nbtor_refined	0.176
r_mcbond_other	0.162
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.133
r_chiral_restr	0.096
r_nbtor_other	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_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	4101
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	108

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling