3NM9

HMGD(M13A)-DNA complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	297	1.2 mM HMGDM13A protein, 1.18 mM duplex DNA fragment (GCGATATCGC), 5 mM MES-Na pH 5.25, 10 mM NaCl, and 7.6% PEG 3350 equilibrated against 0.5 mL 32% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.75	α = 92.49
b = 71.7	β = 91.12
c = 89.02	γ = 107.1

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	IMAGE PLATE	RIGAKU RAXIS IV++	Blue Optics	2001-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.8	20	92.3	0.06	21.9	2.6		23992

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.91	82.1		0.208	4.6

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	1qrv	2.85	20	21700	1179	93.06	0.24763	0.24499	0.29556	RANDOM	58.037

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]
-4.41	-0.6	-1.28	0.4	-4.37	3.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.763
r_dihedral_angle_3_deg	23.877
r_dihedral_angle_4_deg	21.277
r_dihedral_angle_1_deg	4.973
r_scangle_it	4.279
r_scbond_it	3.078
r_mcangle_it	2.821
r_mcbond_it	1.681
r_angle_refined_deg	1.334
r_symmetry_hbond_refined	0.346
r_nbtor_refined	0.298
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.167
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3510
Nucleic Acid Atoms	2042
Solvent Atoms	4
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling