9HB1 | pdb_00009hb1

Structure of IdeC protease C94S from Streptococcus canis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	30% PEG 3350, 200 mM MgCl2 and 100 mM Tris HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.253	α = 90
b = 70.253	β = 90
c = 94.884	γ = 120

Symmetry
Space Group	P 32 2 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		2019-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	ALBA	XALOC

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	2.7	47.44	99.9	0.138	0.977	4.8	9.5		7819

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	2.7	2.83	100		0.792	0.447	1	9.5

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.7	37.44	7793	360	99.872	0.205	0.2017	0.2051	0.2675	0.2706	48.865

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]
1.354	0.677		1.354		-4.391

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.653
r_dihedral_angle_6_deg	14.355
r_lrange_it	6.997
r_lrange_other	6.976
r_dihedral_angle_1_deg	6.07
r_scangle_it	4.783
r_scangle_other	4.706
r_mcangle_it	4.451
r_mcangle_other	4.449
r_scbond_it	2.825
r_scbond_other	2.769
r_mcbond_it	2.646
r_mcbond_other	2.644
r_dihedral_angle_2_deg	2.303
r_angle_refined_deg	1.08
r_angle_other_deg	0.393
r_symmetry_nbd_other	0.211
r_nbd_refined	0.21
r_nbd_other	0.203
r_symmetry_nbd_refined	0.199
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.05
r_symmetry_xyhbond_nbd_other	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2305
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	25

Software

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