9QT2 | pdb_00009qt2

Bacterial histone HLp from Leptospira perolatii bound to DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9QT0	protein without DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Carboxylic acids, 0.1 M Morpheus Buffer System 3, pH 8.5 and 50% (v/v) Morpheus Precipitant Mix 4

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.769	α = 90
b = 91.613	β = 90
c = 100.33	γ = 90

Symmetry
Space Group	F 2 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 16M		2023-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	SLS	X10SA

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	1.9	39.56	68.4	0.06	1	13.86	7.51		6179

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	1.9	2.05	20		1.534	0.426	1.34	6.44

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 (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	1.9	39.56	5261	918	68.35	0.24269	0.23492	0.2391	0.28794	0.2881	RANDOM	45.919

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]
0.33			0.28		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.567
r_dihedral_angle_4_deg	17.549
r_dihedral_angle_3_deg	13.195
r_long_range_B_refined	5.373
r_long_range_B_other	5.365
r_scangle_other	4.09
r_dihedral_angle_1_deg	4.041
r_mcangle_it	2.608
r_mcangle_other	2.608
r_scbond_it	2.587
r_scbond_other	2.585
r_mcbond_it	1.775
r_mcbond_other	1.767
r_angle_other_deg	1.35
r_angle_refined_deg	1.173
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	429
Nucleic Acid Atoms	305
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing
REFMAC	refinement