3B3D | pdb_00003b3d

B.subtilis YtbE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	289	0.1M Bis-Tris pH 6.3, 50mM calcium chloride, 20% PEGMME550, vapor diffusion, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.106	α = 90
b = 89.17	β = 90
c = 115.687	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	Mar			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 3W1A	1.2579	BSRF	3W1A

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	2.3	50	97.2	0.121	5.3	9.4		37940

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)
1	2.3	2.38	100		0.387		9.6	3810

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	20	35898	1885	97.23	0.19586	0.19232	0.2	0.26037	0.27	RANDOM	25.34

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]
1.52			0.15		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.301
r_dihedral_angle_4_deg	24.795
r_dihedral_angle_3_deg	19.5
r_dihedral_angle_1_deg	6.663
r_scangle_it	3.28
r_scbond_it	2.213
r_angle_refined_deg	1.733
r_mcangle_it	1.292
r_mcbond_it	0.784
r_symmetry_hbond_refined	0.317
r_nbtor_refined	0.304
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.159
r_chiral_restr	0.142
r_metal_ion_refined	0.034
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6697
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction