7VCN | pdb_00007vcn

Crystal Structure of PitA fragment from pilus islet-2 of Streptococcus oralis with Tb-Xo4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	295	0.2 M ammonium acetate 0.1 M HEPES pH 7.2, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.815	α = 79.883
b = 70.288	β = 86.895
c = 82.71	γ = 87.186

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.42379	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.343	69.235	82.6	0.065	0.03	0.998	15.7	5.6		38153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.343	2.608			0.552	0.252	0.881

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.343	69.139	38153	1787	66.425	0.196	0.1942	0.19	0.2396	0.24	62.857

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]
0.747	-0.162	-1.082	-0.291	0.637	-0.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.611
r_dihedral_angle_3_deg	17.108
r_dihedral_angle_4_deg	16.95
r_lrange_it	10.855
r_dihedral_angle_1_deg	7.647
r_scangle_it	6.603
r_mcangle_it	5.356
r_scbond_it	4.206
r_mcbond_it	3.226
r_angle_refined_deg	1.82
r_nbtor_refined	0.308
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.209
r_xyhbond_nbd_refined	0.143
r_ncsr_local_group_1	0.13
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.121
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7581
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing