5JEZ

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	6% PEG-8000, 100mM Na Cacodylate pH6.5, 350mM Zn acetate

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.15	α = 90
b = 65.55	β = 90
c = 88.84	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	ADSC QUANTUM 4r		2008-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.7	50	98.4	0.087	15.88	7.24		26908		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	1.7	1.8	96.9		0.475	4.45	7.28

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	2AIE	1.7	44.41	25415	1338	98.5	0.15	0.149	0.188	RANDOM	16.81

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]
0.32			0.84		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.228
r_dihedral_angle_4_deg	20.932
r_dihedral_angle_3_deg	11.634
r_long_range_B_refined	7.72
r_long_range_B_other	6.793
r_dihedral_angle_1_deg	6.52
r_scangle_other	3.101
r_angle_refined_deg	2.514
r_scbond_it	2.042
r_scbond_other	2.04
r_mcangle_other	1.542
r_mcangle_it	1.535
r_angle_other_deg	1.231
r_mcbond_it	1.057
r_mcbond_other	1.039
r_chiral_restr	0.38
r_bond_refined_d	0.033
r_gen_planes_refined	0.016
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1600
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
FRODO	model building
PHASER	phasing