7CY7

Crystal Structure of CMD1 in complex with DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	290	15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.613	α = 90
b = 125.764	β = 102.82
c = 64.034	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 PILATUS3 S 6M		2020-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NFPSS BEAMLINE BL19U1	0.9785	NFPSS	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.15	50.01	96.7	0.067	1	15.8	6.6		60566

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21			0.52	0.82	2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7CY4	2.15	50.01	57529	3035	94.05	0.1896	0.1879	0.2206	RANDOM	40.4

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]
2.87		-0.62	-3.82		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.815
r_sphericity_free	26.609
r_sphericity_bonded	20.093
r_dihedral_angle_4_deg	19.479
r_dihedral_angle_3_deg	14.943
r_dihedral_angle_1_deg	5.596
r_rigid_bond_restr	3.986
r_angle_refined_deg	1.118
r_angle_other_deg	0.993
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6624
Nucleic Acid Atoms	327
Solvent Atoms	402
Heterogen Atoms	37

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing