Experiment: 2NYG

Crystal structure of YokD protein from Bacillus subtilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	273	25% PEG 3350, 0.2M Lithium sulphate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.02	α = 90
b = 132.39	β = 90
c = 185.8	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 210	mirrors	2006-08-14	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210	mirrors	2006-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C		NSLS	X12C
2	SYNCHROTRON	NSLS BEAMLINE X12C		NSLS	X12C

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
1,2	2.37	50	96.4	0.073	11.6	12.1	72328	72328			42.2

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)
	2.37	2.45	82.7		0.49		7.1	6130

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.6	49.04	56032	56032	1145	99.6	0.257	0.257	0.2553	0.296	0.295	RANDOM	52.3

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]
11.8			-12.78		0.98

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_scangle_it	2.75
c_mcangle_it	2.04
c_scbond_it	1.82
c_angle_deg	1.5
c_mcbond_it	1.22
c_improper_angle_d	0.92
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12101
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	210

Software

Software
Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
SHARP	phasing