7YDW

Crystal structure of the MPND-DNA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YDT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG4000, sodium citrate, ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.783	α = 72.583
b = 62.922	β = 89.876
c = 69.085	γ = 89.976

Symmetry
Space Group	P 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 2M		2020-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.9793	SSRF	BL10U2

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	2.47	50	96	0.968	9.5	3.4		21839

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	2.47	2.51			0.894	9.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7YDT	2.47	33.44	20906	1107	95.93	0.246	0.2454	0.2536	46.658

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]
-2.596	-1.187	0.543	-5.688	-1.263	6.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.768
r_dihedral_angle_4_deg	14.714
r_dihedral_angle_3_deg	14.634
r_lrange_it	6.071
r_lrange_other	6.059
r_dihedral_angle_1_deg	5.691
r_mcangle_it	3.961
r_mcangle_other	3.96
r_scangle_it	3.429
r_scangle_other	3.429
r_mcbond_it	2.388
r_mcbond_other	2.388
r_scbond_it	1.979
r_scbond_other	1.979
r_angle_other_deg	1.186
r_angle_refined_deg	1.181
r_nbd_refined	0.185
r_symmetry_nbd_other	0.168
r_nbd_other	0.16
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_nbd_refined	0.113
r_symmetry_nbtor_other	0.076
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	2841
Nucleic Acid Atoms	409
Solvent Atoms	161
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing