2HIY

The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. (CASP Target)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	0.1M Tris pH8.5, 0.2M MgCl2, 25% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.252	α = 90
b = 108.845	β = 97.15
c = 65.527	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	ADSC QUANTUM 315		2005-12-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97906, 0.97923	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	48.28	98.23			160902	160902	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	94.4		2	5.5

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	MAD	THROUGHOUT	1.4	48.28	160902	160902	8487	98.23	0.16427	0.16427	0.16269	0.19439	RANDOM	20.701

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]
-0.28		0.05	-0.49		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.709
r_dihedral_angle_4_deg	17.19
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_1_deg	5.436
r_scangle_it	3.587
r_scbond_it	2.535
r_mcangle_it	1.506
r_angle_refined_deg	1.42
r_mcbond_it	1.01
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.709
r_dihedral_angle_4_deg	17.19
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_1_deg	5.436
r_scangle_it	3.587
r_scbond_it	2.535
r_mcangle_it	1.506
r_angle_refined_deg	1.42
r_mcbond_it	1.01
r_nbtor_refined	0.314
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.168
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.106
r_metal_ion_refined	0.054
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5950
Nucleic Acid Atoms
Solvent Atoms	1657
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
ARP/wARP	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.