4LID | pdb_00004lid

A100, A DNA binding scaffold from Sulfolobus spindle-shape virus 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	296	10mg/ml A100, 0.6-0.9M Ammonium dihydrogen phosphate, 20-30% Glycerol, 0.7M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
2	VAPOR DIFFUSION, HANGING DROP	5.6	296	10mg/ml selenomethionine incorporated A100,0.6-0.9M Ammonium dihydrogen phosphate, 20-30% Glycerol, 0.7M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.999	α = 90
b = 152.999	β = 90
c = 61.727	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	102.5	PIXEL	DECTRIS PILATUS 6M	K-B focusing mirrors	2013-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3	38.25	99.9	0.014	0.047	7.93	12.5	8956	8953	2	1	94.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.16	100		0.688	0.2	5.2	12.5	1263

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	3	21	2	8957	8488	423	99.5	0.2857	0.23767	0.23707	0.2396	0.25062	0.2467	RANDOM	122.806

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]
0.25	0.25		0.25		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.516
r_dihedral_angle_3_deg	16.32
r_dihedral_angle_4_deg	9.045
r_dihedral_angle_1_deg	6.546
r_angle_other_deg	2.96
r_angle_refined_deg	1.743
r_chiral_restr	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1438
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
autoXDS	data reduction
SCALA	data scaling
PHENIX	phasing