8BBM | pdb_00008bbm

DNA binding domain of J-DNA Binding Protein 1 (JBP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XSE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	15-17% Peg 6000, 0.1M Sodium iodide or 15-17% Peg, 0.2M potassium nitrate

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.286	α = 90
b = 68.286	β = 90
c = 185.842	γ = 120

Symmetry
Space Group	P 61 2 2

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 9M		2018-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.98	NSLS-II	17-ID-1

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	1.95	29.6	100	0.157	17.5	38.4		19605			32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			5.033

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	2XSE	1.95	29.59	18522	1017	99.93	0.20453	0.20204	0.21	0.25194	0.26	RANDOM	54.275

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]
0.77	0.39		0.77		-2.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.11
r_dihedral_angle_3_deg	13.895
r_dihedral_angle_4_deg	11.894
r_long_range_B_refined	7.393
r_long_range_B_other	7.345
r_dihedral_angle_1_deg	5.09
r_scangle_other	4.379
r_mcangle_it	3.227
r_mcangle_other	3.227
r_scbond_it	2.762
r_scbond_other	2.759
r_mcbond_it	2.13
r_mcbond_other	2.119
r_angle_refined_deg	1.621
r_angle_other_deg	1.142
r_chiral_restr	0.097
r_bond_refined_d	0.013
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	1400
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms

Software

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