9OW2 | pdb_00009ow2

Crystal Structure of the Surface Protein (CD630_07380) from Clostridium difficile Strain 630

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q189T6-F1	UniProt

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	Protein: 8.4 mg/ml, 0.25M Sodium chloride, 0.01M Tris buffer pH 8.3; Screen: JSCG+ (H8), 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350; Cryo: 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.08	α = 90
b = 94.872	β = 89.99
c = 57.093	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD		2018-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.85	30	100	0.107	0.107	0.122	0.059	1	13.1	4.3		37762		-3	24.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	100		0.988	0.988	0.548	0.656	1.9	4.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	28.55	35814	1924	99.08	0.18146	0.1792	0.1915	0.22399	0.2345	RANDOM	28.106

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]
-15.14		-4.85	31.54		-16.4

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	6.84
r_long_range_B_other	6.833
r_dihedral_angle_3_deg	5.472
r_scangle_other	4.875
r_mcangle_it	3.762
r_mcangle_other	3.762
r_scbond_it	3.208
r_scbond_other	3.207
r_dihedral_angle_1_deg	2.552
r_mcbond_it	2.548
r_mcbond_other	2.548
r_angle_refined_deg	1.42
r_dihedral_angle_2_deg	1.317
r_angle_other_deg	0.494
r_chiral_restr	0.081
r_gen_planes_refined	0.012
r_gen_planes_other	0.01
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	4211
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing