2XD7 | pdb_00002xd7

Crystal structure of the macro domain of human core histone H2A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YD9	PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID
experimental model	PDB	1ZR3	PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID
experimental model	PDB	1ZR5	PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID
experimental model	PDB	3IID	PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.05M MGCL2; 0.1M HEPES PH 7.5; 30% MPEG 550

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.03	α = 90
b = 61.64	β = 89.64
c = 242.23	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	ADSC CCD		2009-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	2.1	41.86	92.7	0.07	7.5	2.4		45536		2	32.2

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	2.1	2.21	77.7		0.37	2.3	2.3

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID	2.09	40	43253	2281	90.55	0.21922	0.21743	0.21	0.25298	RANDOM	33.822

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]
1.93		0.32	-10.95		9.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.208
r_dihedral_angle_3_deg	17.054
r_dihedral_angle_4_deg	12.436
r_dihedral_angle_1_deg	6.203
r_angle_refined_deg	1.45
r_angle_other_deg	1.314
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5584
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing