2HIY | pdb_00002hiy

The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae.

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.161	0.19439	0.1922	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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.