4XEA | pdb_00004xea

Crystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.17 M Na acetate, 0.085 M Tris/HCl, pH 8.5, 25.5% PEG4000, 15% glycerol,chymotrypsin treated

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.201	α = 90
b = 127.201	β = 90
c = 65.991	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 315r	mirrors	2013-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97915	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	30	99.9	0.111	0.117	0.035	23.447	11.5		40177		-3

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	1.95	1.98	100		0.431	0.754	2.03	11.4	1973

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	SAD	THROUGHOUT	1.95	29.29	39985	1075	99.57	0.1824	0.1815	0.1882	0.214	0.2212	RANDOM	47.605

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]
-0.81			-0.81		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.004
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	14.621
r_dihedral_angle_1_deg	6.111
r_scangle_it	3.475
r_scbond_it	2.254
r_angle_refined_deg	1.366
r_mcangle_it	1.271
r_angle_other_deg	0.868
r_mcbond_it	0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.004
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	14.621
r_dihedral_angle_1_deg	6.111
r_scangle_it	3.475
r_scbond_it	2.254
r_angle_refined_deg	1.366
r_mcangle_it	1.271
r_angle_other_deg	0.868
r_mcbond_it	0.71
r_mcbond_other	0.214
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3386
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	22

Software

Software
Software Name	Purpose
SBC-Collect	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing
ARP	model building
SHELX	phasing
DM	phasing
HKL-3000	data reduction
WARP	model building
SHELX	model building
DM	model building

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.