3B6F | pdb_00003b6f

Nucleosome core particle treated with cisplatin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KX5	PDB entry 1KX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.327	α = 90
b = 109.38	β = 90
c = 180.585	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	98	CCD	MARMOSAIC 225 mm CCD		2007-02-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.072	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.45	93.66	99.1	0.076	0.076	5.5	7.3		28162		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.45	3.64	100		0.485	0.485	1.4	7.5	4098

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB entry 1KX5	3.45	93.66	28106	588	98.88	0.331	0.33	0.402	RANDOM	185.185

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]
3.59			-17.45		13.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.374
r_dihedral_angle_3_deg	20.063
r_dihedral_angle_4_deg	19.254
r_dihedral_angle_1_deg	6.309
r_angle_refined_deg	1.245
r_mcangle_it	1.244
r_scangle_it	1.091
r_mcbond_it	0.683
r_scbond_it	0.607
r_nbtor_refined	0.305
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.187
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6269
Nucleic Acid Atoms	6021
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction