3LJA

Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.348	α = 90
b = 109.785	β = 90
c = 182.424	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2007-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.89	SLS	X06SA

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	2.75	76.5	95.8	0.085	21.2	6.8		53707

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	2.75	2.9	89.5		0.425	3.6	6.5	7216

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 1KX5	2.75	38.19	52580	1078	95.38	0.22324	0.2225	0.25904	RANDOM	54.531

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]
1.36			-2.8		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.624
r_dihedral_angle_4_deg	20.164
r_dihedral_angle_3_deg	16.676
r_dihedral_angle_1_deg	4.932
r_scangle_it	2.138
r_angle_refined_deg	1.475
r_scbond_it	1.322
r_mcangle_it	1.317
r_mcbond_it	0.687
r_nbtor_refined	0.312
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.082
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6156
Nucleic Acid Atoms	6021
Solvent Atoms
Heterogen Atoms	60

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling