7C7X

Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.71	α = 90
b = 128.396	β = 90
c = 140.275	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	PIXEL	DECTRIS EIGER X 16M		2017-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9793	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	30	96.9	0.093	0.099	0.033	7.4	7.6		24251

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	85		0.393	0.452	0.215	0.167		3.6

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	5DAY	3	29.62	20062	1042	84.93	0.2248	0.2229	0.2617	RANDOM	74.159

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]
-1.42			2.82		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.475
r_dihedral_angle_4_deg	22.414
r_dihedral_angle_3_deg	21.388
r_dihedral_angle_1_deg	7.963
r_angle_refined_deg	1.54
r_angle_other_deg	1.258
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.475
r_dihedral_angle_4_deg	22.414
r_dihedral_angle_3_deg	21.388
r_dihedral_angle_1_deg	7.963
r_angle_refined_deg	1.54
r_angle_other_deg	1.258
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5454
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.