9QT1 | pdb_00009qt1

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		protein without DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES, PH 7.5 and 25% PEG 6000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.934	α = 90
b = 67.934	β = 90
c = 97.902	γ = 90

Symmetry
Space Group	P 41 21 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		2023-08-24	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	2.1	43.16	99.7	0.081	0.999	11.09	5.62		13927

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	2.1	2.23	99.5		0.743	0.84	1.96	5.53

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	2.1	43.16	13229	696	99.64	0.2513	0.24983	0.2609	0.27946	0.2959	RANDOM	55.889

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]
-2.74			-2.74		5.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.895
r_dihedral_angle_3_deg	18.213
r_dihedral_angle_4_deg	13.388
r_long_range_B_refined	10.499
r_long_range_B_other	10.481
r_scangle_other	6.912
r_scbond_it	4.754
r_scbond_other	4.702
r_dihedral_angle_1_deg	4.331
r_mcangle_other	4.156
r_mcangle_it	4.152
r_mcbond_it	3.016
r_mcbond_other	3.003
r_angle_other_deg	1.457
r_angle_refined_deg	1.297
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	870
Nucleic Acid Atoms	656
Solvent Atoms	47
Heterogen Atoms	10

Software

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