2I58

Crystal Structure of RafE from Streptococcus pneumoniae complexed with raffinose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HQ0	2 models: 2HQ0 residues 1-114 and 278-327 and 2HQ0 residues 115-277 and 328-387

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	25.5% PEG4000 0.085M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.214	α = 90
b = 119.435	β = 90
c = 146.326	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 225 mm CCD	mirrors	2006-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5418

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	2.8	49.21	91.5	0.171	7	6.59	20180	20180

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	2.8	2.9	98.1		0.461	2.7	6.3	2121

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2 models: 2HQ0 residues 1-114 and 278-327 and 2HQ0 residues 115-277 and 328-387	2.8	46.27	20129	20129	971	91.45	0.215	0.211	0.296	Conserved from 2HQ0	47.857

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]
3.46			3.84		-7.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.205
r_dihedral_angle_4_deg	19.697
r_dihedral_angle_3_deg	18.811
r_dihedral_angle_1_deg	7.166
r_mcbond_other	6.141
r_scangle_it	4.69
r_angle_other_deg	4.606
r_mcangle_it	3.175
r_scbond_it	2.921
r_mcbond_it	1.794
r_angle_refined_deg	1.756
r_symmetry_vdw_other	0.306
r_nbd_refined	0.245
r_symmetry_vdw_refined	0.244
r_nbd_other	0.24
r_nbtor_refined	0.2
r_xyhbond_nbd_refined	0.166
r_nbtor_other	0.122
r_chiral_restr	0.094
r_symmetry_hbond_refined	0.084
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6086
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	71

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
d*TREK	data reduction