3CBW | pdb_00003cbw

Crystal structure of the YdhT protein from Bacillus subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	3.5	294	100mM Citric acid pH 3.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.728	α = 90
b = 69.619	β = 91.09
c = 72.505	γ = 90

Symmetry
Space Group	P 1 21 1

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		2008-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.269	72.548	95.5	0.095	0.095	15.1	7.6	145644	145644			9.6

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)
	1.269	1.33	88.5		0.439	0.439	3.3	6.9	19656

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	1.269	20	145624	145624	7331	96.26	0.151	0.149	0.15	0.172	0.18	RANDOM	14.12

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]
0.05		0.09	0.24		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.977
r_dihedral_angle_4_deg	17.23
r_dihedral_angle_3_deg	11.903
r_dihedral_angle_1_deg	5.849
r_sphericity_free	3.14
r_scangle_it	2.608
r_sphericity_bonded	1.829
r_scbond_it	1.821
r_mcangle_it	1.346
r_angle_refined_deg	1.197
r_rigid_bond_restr	1.062
r_mcbond_it	0.873
r_nbtor_refined	0.309
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.142
r_symmetry_vdw_refined	0.132
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5381
Nucleic Acid Atoms
Solvent Atoms	592
Heterogen Atoms	39

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building