2XD5

Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		50 MM HEPES, 3.2 M NACL, 0.8 M AMMONIUM SULFATE, pH 7

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.8	α = 90
b = 101.1	β = 90
c = 145	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		2004-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	2.5	45.91	99.9	0.22	11.46	4.7		49863		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	2.5	2.7	100		0.05		4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 2BG1	2.5	83.05	2	47382	2481	99.9	0.184	0.181	0.233	RANDOM	32.53

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]
-0.6			-0.14		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.87
r_dihedral_angle_3_deg	18.701
r_dihedral_angle_4_deg	18.375
r_dihedral_angle_1_deg	8.006
r_scangle_it	4.466
r_scbond_it	2.937
r_angle_refined_deg	2.182
r_mcangle_it	1.879
r_mcbond_it	1.123
r_nbtor_refined	0.319
r_nbd_refined	0.255
r_symmetry_hbond_refined	0.235
r_chiral_restr	0.22
r_xyhbond_nbd_refined	0.174
r_symmetry_vdw_refined	0.169
r_bond_refined_d	0.025
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	7209
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing