5DEV | pdb_00005dev

High resolution structure of CCG DNA repeats at 1.71 angstrom resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277.15	50 mM Sodium cacodylate, 1 mM magnesium chloride, 3% 2-methylpentane-2,4-diol, 0.5 mM Cobalt(II) chloride

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.228	α = 90
b = 38.228	β = 90
c = 54.227	γ = 90

Symmetry
Space Group	P 43 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	110	CCD	ADSC QUANTUM 315r		2014-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.71	30	99.6	0.035	67.391	13.1		4687

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.77	100		0.474	4	12.9

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	1.71	27.03	4475	216	99.6	0.23	0.227	0.23	0.285	0.28	RANDOM	38.98

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	7.967
r_long_range_B_other	7.917
r_scangle_other	7.265
r_scbond_it	5.605
r_scbond_other	5.594
r_angle_refined_deg	3.753
r_angle_other_deg	2.34
r_chiral_restr	0.15
r_bond_other_d	0.055
r_gen_planes_refined	0.034
r_bond_refined_d	0.028
r_gen_planes_other	0.005
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_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
Nucleic Acid Atoms	218
Solvent Atoms	60
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PHENIX	phasing