9GSO | pdb_00009gso

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

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
2.27	45.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.828	α = 90
b = 59.678	β = 90
c = 67.288	γ = 90

Symmetry
Space Group	P 2 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 PILATUS3 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)	CC (Half)	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	1.615	44.648	100	0.078	0.999	13.4	6.3		24706			21.9

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	1.62	1.64			1.97	0.142	0.79

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.615	44.648	24670	1211	99.312	0.192	0.1903	0.1996	0.2219	0.2269	31.777

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]
-1.531			0.638		0.893

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.566
r_dihedral_angle_1_deg	13.922
r_dihedral_angle_3_deg	11.891
r_lrange_it	7.143
r_lrange_other	7.105
r_scangle_it	5.09
r_scangle_other	5.088
r_mcangle_it	3.535
r_mcangle_other	3.535
r_scbond_it	3.225
r_scbond_other	3.223
r_mcbond_it	2.208
r_mcbond_other	2.187
r_angle_refined_deg	1.24
r_angle_other_deg	0.499
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_refined	0.202
r_nbtor_refined	0.177
r_symmetry_nbd_other	0.155
r_xyhbond_nbd_refined	0.144
r_symmetry_nbd_refined	0.121
r_nbd_other	0.106
r_symmetry_nbtor_other	0.065
r_chiral_restr	0.059
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1375
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms

Software

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