7BP2 | pdb_00007bp2

Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.2M Sodium sulphate 0.1M Bis Tris propane pH 7.5 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.86	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.712	α = 90
b = 65.712	β = 90
c = 96.687	γ = 120

Symmetry
Space Group	P 31

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		2018-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97853	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	1.58	30	99.9	0.049	0.052	0.016	12.3	8.7		64079

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	1.58	1.64	99.9		0.299	0.321	0.116	0.932		7.1

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	1AOI	1.58	28.45	60749	3127	99.86	0.1564	0.1549	0.1677	0.1863	0.1941	RANDOM	16.962

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]
-0.32			-0.32		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.334
r_dihedral_angle_4_deg	20.096
r_dihedral_angle_3_deg	14.2
r_dihedral_angle_1_deg	5.884
r_angle_refined_deg	1.295
r_angle_other_deg	1.274
r_chiral_restr	0.091
r_gen_planes_refined	0.02
r_bond_refined_d	0.018
r_gen_planes_other	0.013
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2722
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms	74

Software

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