2OGI

Crystal structure of a putative metal dependent phosphohydrolase (sag1661) from streptococcus agalactiae serogroup v at 1.85 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	277	NANODROP, 1.0M LiCl, 20.0% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.841	α = 90
b = 52.535	β = 114.29
c = 70.022	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)	2006-12-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97935, 0.97864	SSRL	BL11-1

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	1.85	40.555	99.6	0.073	11.13			37403			32.44

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	1.85	1.92	98.9		0.658	2

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	1.85	40.55	37389	1865	99.8	0.174	0.172	0.229	RANDOM	28.84

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]
1.6		-1.2	-0.27		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.084
r_dihedral_angle_4_deg	19.576
r_dihedral_angle_3_deg	15.105
r_scangle_it	7.054
r_dihedral_angle_1_deg	5.734
r_scbond_it	5.18
r_mcangle_it	3.026
r_mcbond_it	2.051
r_angle_refined_deg	1.653
r_angle_other_deg	0.9
r_mcbond_other	0.632
r_symmetry_vdw_other	0.227
r_nbd_refined	0.222
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.191
r_symmetry_hbond_refined	0.183
r_nbd_other	0.178
r_symmetry_vdw_refined	0.125
r_chiral_restr	0.094
r_nbtor_other	0.087
r_metal_ion_refined	0.049
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3089
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	75

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