2POK

Crystal structure of a M20 family metallo peptidase from Streptococcus pneumoniae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	0.2M Ammonium acetate, 0.5M Sodium chloride, 20% w/v PEG 3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.954	α = 90
b = 101.922	β = 90
c = 118.074	γ = 90

Symmetry
Space Group	P 21 21 21

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 300 mm CCD	mirrors	2006-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0000	APS	23-ID-D

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	1.9	25	99.6	0.062	17.1	3.7	83179	83179		-3

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	1.9	1.97	100		0.367	2.9	3.7	8229

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	MIRAS	THROUGHOUT	1.9	25	79025	4150	99.42	0.18053	0.1781	0.22579	RANDOM	28.493

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]
-2.86			-1.66		4.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.26
r_dihedral_angle_4_deg	15.662
r_dihedral_angle_3_deg	12.401
r_scangle_it	5.081
r_dihedral_angle_1_deg	4.784
r_scbond_it	3.222
r_mcangle_it	1.94
r_angle_refined_deg	1.555
r_mcbond_it	1.289
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.26
r_dihedral_angle_4_deg	15.662
r_dihedral_angle_3_deg	12.401
r_scangle_it	5.081
r_dihedral_angle_1_deg	4.784
r_scbond_it	3.222
r_mcangle_it	1.94
r_angle_refined_deg	1.555
r_mcbond_it	1.289
r_nbtor_refined	0.321
r_xyhbond_nbd_refined	0.223
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.21
r_symmetry_hbond_refined	0.202
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7261
Nucleic Acid Atoms
Solvent Atoms	817
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

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.