9FT8 | pdb_00009ft8

Crystal structure of d(CGTGAATTCACG) with HT1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JU4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	10%MPD, 60mM MgCl2, 30 mM NaCaCo (pH6.8), 1mM Spermine

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.593	α = 90
b = 40.406	β = 90
c = 65.033	γ = 90

Symmetry
Space Group	P 21 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	294	PIXEL	DECTRIS PILATUS 2M		2022-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	2	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.902	34.321	99.8	0.964	4.36	7		5462			39.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.902	1.951			0.964

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	1.902	34.321	5451	251	99.817	0.221	0.2193	0.2265	0.2465	0.2595	37.124

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]
-0.002			-0.001		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	8.776
r_lrange_it	8.586
r_scangle_it	4.823
r_scangle_other	4.82
r_scbond_it	3.49
r_scbond_other	3.488
r_angle_refined_deg	1.809
r_angle_other_deg	1.691
r_metal_ion_refined	0.285
r_symmetry_nbd_refined	0.276
r_nbtor_refined	0.247
r_nbd_other	0.217
r_symmetry_nbd_other	0.216
r_xyhbond_nbd_refined	0.159
r_nbd_refined	0.147
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_refined	0.073
r_gen_planes_refined	0.018
r_bond_other_d	0.016
r_bond_refined_d	0.009
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	18
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing