8YXN

X-ray structure of Clostridium perfringens autolysin catalytic domain in the P1 form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	10% (w/v) PEG 3000, 100mM CHES/ sodium hydroxide

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.13	α = 94.79
b = 47.52	β = 89.916
c = 64.31	γ = 96.29

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	IMAGE PLATE	RIGAKU RAXIS VII		2016-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	36.53	98.9	0.995	7.5	5.6		56867

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64			0.809

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	36.503	56867	2811	98.904	0.165	0.1629	0.1968	19.429

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]
0.016	0.001	0.004	-0.04	0.012	0.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.688
r_dihedral_angle_4_deg	17.901
r_dihedral_angle_3_deg	14.114
r_dihedral_angle_1_deg	6.192
r_lrange_it	5.389
r_lrange_other	5.262
r_scangle_other	3.561
r_scangle_it	3.56
r_mcangle_other	2.859
r_mcangle_it	2.856
r_scbond_it	2.326
r_scbond_other	2.323
r_mcbond_it	1.898
r_mcbond_other	1.88
r_angle_refined_deg	1.634
r_angle_other_deg	1.476
r_nbd_refined	0.217
r_nbd_other	0.207
r_symmetry_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.089
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4076
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms

Software

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