1YSJ

Crystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding Peptidase from M20 Family

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XMB	pdb entry 1xmb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.25M NaCl, 0.1M MES, 25% PEG 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 233.854	α = 90
b = 42.157	β = 106.713
c = 75.449	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARRESEARCH	MIRROR	2004-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	0.97857	APS	32-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	30	98.5	0.074	13.4	3.5	28357	28357		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	87.7		0.362	2.5	2.5	2508

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1xmb	2.4	25	26357	1427	98.88	0.18501	0.18173	0.24709	RANDOM	45.265

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]
-0.8		-0.6	0.85		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.845
r_dihedral_angle_4_deg	15.844
r_dihedral_angle_3_deg	14.405
r_dihedral_angle_1_deg	4.865
r_scangle_it	4.691
r_scbond_it	3.076
r_mcangle_it	1.721
r_mcbond_it	1.293
r_angle_refined_deg	0.914
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.845
r_dihedral_angle_4_deg	15.844
r_dihedral_angle_3_deg	14.405
r_dihedral_angle_1_deg	4.865
r_scangle_it	4.691
r_scbond_it	3.076
r_mcangle_it	1.721
r_mcbond_it	1.293
r_angle_refined_deg	0.914
r_nbtor_refined	0.294
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.142
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.1
r_chiral_restr	0.063
r_metal_ion_refined	0.027
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5539
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.