9GSQ

DNA binding domain of J-DNA Binding Protein 3 (JBP3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		OneDep ID : D_1292141777

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.2 M potassium sodium tartrate tetrahydrate, 20% w/v polyethylane glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.701	α = 90
b = 40.937	β = 123.816
c = 100.595	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	PIXEL	DECTRIS PILATUS 6M		2017-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.966	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.7	83.576	99	0.05	11.1	2.9		41694			23.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.63	0.736	0.75	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	83.576	41665	2114	98.357	0.176	0.174	0.2116	34.999

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]
-0.95		-0.421	0.315		0.632

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.252
r_dihedral_angle_3_deg	11.904
r_lrange_other	10.887
r_lrange_it	10.87
r_dihedral_angle_1_deg	8.689
r_scangle_it	8.155
r_scangle_other	8.151
r_scbond_it	5.492
r_scbond_other	5.491
r_mcangle_it	5.47
r_mcangle_other	5.468
r_mcbond_it	3.715
r_mcbond_other	3.708
r_angle_refined_deg	1.164
r_angle_other_deg	0.449
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.215
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.17
r_nbd_other	0.166
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.141
r_ncsr_local_group_1	0.112
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3109
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB-REDO	refinement