Experiment: 3C21

Structure of a bacterial DNA damage sensor protein with reaction product

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C1Y	PDB ENTRY 3C1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M Tris, 0.2M Ammoniumacetate, 35% MPD, 3mM ATP-gammaS, 3mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.08	α = 90
b = 109.08	β = 90
c = 165.88	γ = 90

Symmetry
Space Group	P 4 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	100	CCD	MARMOSAIC 225 mm CCD		2006-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0099	SLS	X06SA

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	2.7	30	98.2	0.075	0.079	24.51	9.63	27866	27866

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)
	2.7	2.86	96.6		0.355	0.379	7.19	9.5	4315

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3C1Y	2.7	30	27823	2762	98.6	0.208	0.2072	0.269	0.2696	RANDOM	42.631

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]
4.13			4.13		-8.26

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.406
c_mcangle_it	2.23
c_scbond_it	2.165
c_mcbond_it	1.312
c_angle_deg	1.12
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5594
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	44

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing