7VCR

Crystal Structure of PitA fragment 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	7VCN

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
3.22	61.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.48	α = 80.087
b = 70.875	β = 87.024
c = 82.466	γ = 87.7

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		2018-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.97951	ESRF	ID30B

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	81.15	90.3	0.052	0.047	0.999	11.3	3.2		83573

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	2.04	92.1		0.818	0.647	0.727	1.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7VCN	2	69.879	83565	4294	90.314	0.203	0.2009	0.2339	57.196

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]
3.402	-1.455	0.52	-0.696	0.411	-2.472

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.5
r_dihedral_angle_4_deg	19.342
r_dihedral_angle_3_deg	15.642
r_lrange_it	11.076
r_scangle_it	8.553
r_dihedral_angle_1_deg	7.078
r_scbond_it	5.847
r_mcangle_it	5.766
r_mcbond_it	4.09
r_angle_refined_deg	1.925
r_nbtor_refined	0.306
r_nbd_refined	0.196
r_symmetry_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.144
r_chiral_restr	0.139
r_xyhbond_nbd_refined	0.129
r_ncsr_local_group_1	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7586
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing