5JEY

Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in cacodylate buffer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	9% PEG-8000, 100mM Na Cacodylate pH6.5, 100mM Zn acetate

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.36	α = 90
b = 65.98	β = 90
c = 89.45	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		2008-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	2.78	50	98	0.159	8.8	2.55		11619	2	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	2.78	2.95	93.2		0.48	3.43	2.44

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	2.8	37.53	6079	320	100	0.18535	0.18197	0.24787	RANDOM	32.437

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]
-0.72			0.86		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.309
r_dihedral_angle_4_deg	31.881
r_dihedral_angle_3_deg	19.323
r_scangle_it	7.782
r_dihedral_angle_1_deg	7.23
r_scbond_it	4.908
r_angle_refined_deg	2.606
r_mcangle_it	2.485
r_mcbond_it	1.556
r_symmetry_hbond_refined	0.415
r_nbtor_refined	0.331
r_symmetry_vdw_refined	0.263
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.221
r_metal_ion_refined	0.147
r_chiral_restr	0.137
r_bond_refined_d	0.03
r_gen_planes_refined	0.01
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_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	1567
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	8

Software

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