3DI4

Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3 at 1.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	1.7M ammonium sulfate, 2.0% polyethylene glycol 400, 15.0% Glycerol, 0.1M HEPES pH 6.9, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.465	α = 90
b = 95.764	β = 109.04
c = 58.689	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-05-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97941,0.97904	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	1.6	28.41	98.3	0.072	0.072	7	2.6		69473			15.579

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	1.6	1.64	94		0.444	0.444	1.7	2.5	4868

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.6	28.41	69445	3499	98.15	0.142	0.141	0.175	RANDOM	12.623

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]
0.03		0.24	0.1		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.066
r_dihedral_angle_4_deg	15.417
r_dihedral_angle_3_deg	11.904
r_dihedral_angle_1_deg	6.127
r_scangle_it	4.587
r_scbond_it	3.317
r_mcangle_it	2.302
r_mcbond_it	1.616
r_angle_refined_deg	1.539
r_angle_other_deg	0.989
r_mcbond_other	0.57
r_symmetry_vdw_other	0.306
r_symmetry_vdw_refined	0.217
r_nbd_other	0.21
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.195
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_other	0.145
r_chiral_restr	0.095
r_nbtor_other	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4245
Nucleic Acid Atoms
Solvent Atoms	739
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing