6S6H | pdb_00006s6h

Crystal structure of the DNA binding domain of the chromosome-partitioning protein ParB complexed to the centromeric parS site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UMK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.099	α = 90
b = 40.717	β = 121.4
c = 94.004	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-F		2018-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.4	40.12	99.7	0.137	0.15	0.058	0.992	7	6.4		16317

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	2.4	2.49	99.2		0.801	0.869	0.333	0.85		6.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4UMK	2.4	40.12	15480	826	99.35	0.2169	0.2161	0.2206	0.2322	0.2432	RANDOM	48.259

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]
-3.09		-1.86	2.82		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.98
r_dihedral_angle_4_deg	20.987
r_dihedral_angle_3_deg	14.037
r_dihedral_angle_1_deg	5.104
r_angle_other_deg	1.193
r_angle_refined_deg	1.087
r_chiral_restr	0.044
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1917
Nucleic Acid Atoms	814
Solvent Atoms	82
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing