3DNX

SPO1766 protein of unknown function from Silicibacter pomeroyi.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	2.5 M sodium chloride, 0.1 M sodium/potassium phosphate buffer, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.892	α = 90
b = 59.892	β = 90
c = 99.868	γ = 90

Symmetry
Space Group	P 41 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	ADSC QUANTUM 315		2008-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	1.94	39	100	0.106	10.2	10.8	14100	14100			39.1

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	1.94	1.97	100		0.82	3.01	11.1	680

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.94	39	14043	14043	698	99.91	0.174	0.174	0.172	0.213	RANDOM	34.766

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]
-0.73			-0.73		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.359
r_dihedral_angle_4_deg	24.457
r_dihedral_angle_3_deg	18.655
r_dihedral_angle_1_deg	6.134
r_scangle_it	3.77
r_scbond_it	2.317
r_mcangle_it	1.572
r_angle_refined_deg	1.523
r_angle_other_deg	0.96
r_mcbond_it	0.892
r_symmetry_vdw_other	0.317
r_mcbond_other	0.237
r_xyhbond_nbd_refined	0.23
r_nbd_refined	0.209
r_nbd_other	0.209
r_nbtor_refined	0.177
r_metal_ion_refined	0.122
r_symmetry_vdw_refined	0.115
r_symmetry_hbond_refined	0.11
r_nbtor_other	0.094
r_chiral_restr	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1166
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing