2VSI

Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPA	PDB ENTRY 1VPA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.75		100 MM HEPES PH 6.75 35 % V/W PEG 300 200 MM CACL2

Crystal Properties
Matthews coefficient	Solvent content
2.42	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.94	α = 90
b = 92.38	β = 90
c = 143.58	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	140	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS	2008-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU R-AXIS

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	2.75	60.86	99.5	0.09	14.7	3.6		14243		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	2.75	2.9	100		0.52	2.2	3.6

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 1VPA	2.75	56.08	12215	624	89.5	0.215	0.212	0.271	RANDOM	55.38

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]
1.27			-1.99		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.435
r_dihedral_angle_3_deg	17.262
r_dihedral_angle_4_deg	15.458
r_dihedral_angle_1_deg	5.543
r_angle_refined_deg	1.193
r_scangle_it	0.947
r_scbond_it	0.59
r_mcangle_it	0.459
r_nbtor_refined	0.303
r_mcbond_it	0.258
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	3556
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing