2O2Z | pdb_00002o2z

Crystal structure of a protein member of the upf0052 family (bh3568) from bacillus halodurans at 2.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	8.5	277	40.0% polyethylene glycol 400, 0.2M lithium sulfate, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.43	α = 90
b = 143.64	β = 90
c = 233.68	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 315		2006-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	2.6	29.437	99.6	0.083	15.41			54381			45.6

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)
	2.6	2.69	97.5		0.401	2.9

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	SAD	THROUGHOUT	2.6	29.437	54312	2764	99.68	0.19	0.188	0.1964	0.224	0.2328	RANDOM	36.271

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]
-0.86			0.2		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.56
r_dihedral_angle_4_deg	18.814
r_dihedral_angle_3_deg	15.916
r_scangle_it	6.797
r_dihedral_angle_1_deg	5.492
r_scbond_it	4.899
r_mcangle_it	2.6
r_mcbond_it	1.566
r_angle_refined_deg	1.5
r_angle_other_deg	0.92
r_symmetry_vdw_refined	0.342
r_mcbond_other	0.238
r_nbd_refined	0.216
r_nbd_other	0.188
r_nbtor_refined	0.175
r_symmetry_vdw_other	0.174
r_xyhbond_nbd_refined	0.17
r_symmetry_hbond_refined	0.098
r_nbtor_other	0.086
r_xyhbond_nbd_other	0.081
r_chiral_restr	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9095
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	216

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing