2C1I

Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C1G	PDB ENTRY 2C1G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				PROTEIN WAS CRYSTALLIZED FROM 35% PEG 200, 5% PEG 3000, 100 MM MES, PH 6; THEN SOAKED IN 10 MM ZNCL2. FOLLOWED BY SOAK IN 20%PEG 200, 100MM MES, PH 6

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.275	α = 90
b = 79.239	β = 90
c = 100.377	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	MARRESEARCH	MIRROR	2004-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	1.35	15	94.3	0.07	16.8	5.4		93309		2

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	1.35	1.4	94.5		0.44	2.8	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2C1G	1.35	15	91377	1840	94.2	0.189	0.188	0.225	RANDOM	20.78

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]
0.44			-0.02		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.858
r_dihedral_angle_4_deg	18.787
r_dihedral_angle_3_deg	14.448
r_dihedral_angle_1_deg	6.493
r_scangle_it	4.478
r_scbond_it	3.345
r_mcangle_it	2.366
r_mcbond_it	1.697
r_angle_refined_deg	1.569
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.105
r_xyhbond_nbd_refined	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3085
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL	data reduction
HKL	data scaling