3IID | pdb_00003iid

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZR3	PDB entry 1ZR3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	35% PEG 1000, 0.2 M K2NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.26	α = 90
b = 86.26	β = 90
c = 51.04	γ = 120

Symmetry
Space Group	P 61

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		2006-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.973	ESRF	ID29

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	1.9	19.86	99.5	0.057	23.7	10	17128	17128	-3		41

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	1.9	1.95	94.4		0.525	3.6	7.3	1220

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1ZR3	1.9	19.86	16271	857	100	0.17769	0.17579	0.18	0.21467	0.23	RANDOM	32.866

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]
-1.8	-0.9		-1.8		2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.983
r_dihedral_angle_4_deg	22.509
r_dihedral_angle_3_deg	14.206
r_dihedral_angle_1_deg	9.524
r_scangle_it	2.878
r_scbond_it	2.038
r_angle_refined_deg	1.68
r_mcangle_it	1.073
r_angle_other_deg	1.002
r_mcbond_it	0.839
r_nbd_refined	0.232
r_mcbond_other	0.189
r_symmetry_vdw_refined	0.188
r_nbd_other	0.182
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.166
r_symmetry_vdw_other	0.163
r_chiral_restr	0.1
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1377
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	40

Software

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