5FGR | pdb_00005fgr

Crystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG - P21212 space group with Yb Heavy atom

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	0.1M MES, 0.02M zinc sulphate, 25% PEG 550MME, 50mM Yb-DTPA-BMA

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.603	α = 90
b = 75.252	β = 90
c = 117.388	γ = 90

Symmetry
Space Group	P 21 21 2

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		2014-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.28136	ESRF	BM14

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	2.79	45.74	99.8	0.098	22.7	14		13205

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	2.79	2.94	98.8		0.452	7.1	13.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.79	45.74	12523	650	99.73	0.19916	0.19738	0.1999	0.23583	0.2349	RANDOM	62.155

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]
3.19			1.99		-5.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.099
r_dihedral_angle_3_deg	13.838
r_dihedral_angle_4_deg	10.619
r_long_range_B_other	6.916
r_long_range_B_refined	6.914
r_dihedral_angle_1_deg	6.187
r_scangle_other	3.968
r_mcangle_it	2.971
r_mcangle_other	2.97
r_scbond_it	2.405
r_scbond_other	2.405
r_mcbond_it	1.805
r_mcbond_other	1.805
r_angle_refined_deg	1.087
r_angle_other_deg	0.754
r_chiral_restr	0.056
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	3683
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data processing
Aimless	data scaling
PHENIX	phasing
Coot	model building