2Q83 | pdb_00002q83

Crystal structure of ytaA (2635576) from Bacillus subtilis at 2.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.57	277	NANODROP, 2.23M Ammonium sulfate, 0.1M Citric acid pH 5.57, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 172.999	α = 90
b = 172.999	β = 90
c = 192.574	γ = 120

Symmetry
Space Group	P 64 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	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-05-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97904, 0.97932	SSRL	BL11-1

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	2.5	29.961	99.9	0.126	0.126	4.6	10.8		59155			50.53

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	2.5	2.56	100		0.864	0.864	0.9	11	4302

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.5	29.961	59108	2988	99.91	0.199	0.198	0.2	0.21	0.21	RANDOM	40.685

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]
-0.36	-0.18		-0.36		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.805
r_dihedral_angle_3_deg	9.171
r_dihedral_angle_4_deg	9.125
r_scangle_it	6.54
r_scbond_it	4.356
r_mcangle_it	2.556
r_dihedral_angle_1_deg	2.155
r_angle_refined_deg	1.655
r_mcbond_it	1.517
r_angle_other_deg	1.182
r_mcbond_other	0.321
r_symmetry_hbond_refined	0.206
r_nbd_refined	0.178
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.16
r_nbd_other	0.131
r_symmetry_vdw_refined	0.101
r_symmetry_vdw_other	0.092
r_nbtor_other	0.083
r_chiral_restr	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5286
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SOLVE	phasing
RESOLVE	phasing