1XXL

The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	2.4M Am Sulfate, 0.1M Na Citrate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.928	α = 90
b = 74.212	β = 90
c = 246.161	γ = 90

Symmetry
Space Group	C 2 2 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	MAR CCD 165 mm	Diamond monochromator and horizontal, vertical focusing mirrors	2004-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	2.1	20	99.9	0.099	16.66	6.43	37699	37661		-3	28.5

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)
	2.1	2.17	100		0.258	9.35	6.75	3711

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	20	-3	37652	35769	1883	99.78	0.17872	0.17872	0.17638	0.22423	RANDOM	17.301

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]
0.54			0.22		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.959
r_dihedral_angle_4_deg	19.962
r_dihedral_angle_3_deg	15.468
r_dihedral_angle_1_deg	6.057
r_scangle_it	3.954
r_scbond_it	2.689
r_mcangle_it	1.442
r_angle_refined_deg	1.345
r_mcbond_it	1.26
r_angle_other_deg	0.828
r_xyhbond_nbd_other	0.264
r_symmetry_hbond_refined	0.244
r_symmetry_vdw_other	0.216
r_nbd_refined	0.208
r_mcbond_other	0.199
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.172
r_symmetry_vdw_refined	0.11
r_nbtor_other	0.088
r_chiral_restr	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3722
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing