7W6B | pdb_00007w6b

Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VCR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	295	100 mM HEPES pH 7.8, 1 M potassium iodide, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.271	α = 90
b = 422.928	β = 90
c = 48.391	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		2016-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.7712	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	2.984	51.93	95	0.072	0.991	10.6	7		20771

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.984	3.068			0.479	0.577	1.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7VCR	2.984	51.93	20771	1068	90.125	0.256	0.2533	0.25	0.3052	0.31	85.705

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]
2.478			-0.729		-1.749

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.567
r_dihedral_angle_4_deg	20.79
r_dihedral_angle_3_deg	19.753
r_lrange_it	15.007
r_mcangle_it	6.931
r_scangle_it	6.744
r_dihedral_angle_1_deg	6.553
r_mcbond_it	4.041
r_scbond_it	3.981
r_angle_refined_deg	1.558
r_symmetry_nbd_refined	0.373
r_nbtor_refined	0.31
r_metal_ion_refined	0.297
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.105
r_symmetry_xyhbond_nbd_refined	0.095
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5878
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing