3AMI | pdb_00003ami

The crystal structure of the M16B metallopeptidase subunit from Sphingomonas sp. A1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	12% PEG 4000, 0.1M litium sulfate, 0.1M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.405	α = 90
b = 139.757	β = 107.91
c = 63.714	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	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1	SPring-8	BL38B1

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	50	100	0.133	18.33			32754

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	100		0.356	4.47

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	2.4	42.78	31041	1659	99.86	0.19982	0.19622	0.2	0.26586	0.27	RANDOM	37.949

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]
0.77		0.65	-1.08		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.759
r_dihedral_angle_4_deg	18.74
r_dihedral_angle_3_deg	17.676
r_dihedral_angle_1_deg	4.966
r_scangle_it	3.176
r_scbond_it	1.825
r_mcangle_it	1.239
r_angle_refined_deg	0.962
r_mcbond_it	0.648
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.759
r_dihedral_angle_4_deg	18.74
r_dihedral_angle_3_deg	17.676
r_dihedral_angle_1_deg	4.966
r_scangle_it	3.176
r_scbond_it	1.825
r_mcangle_it	1.239
r_angle_refined_deg	0.962
r_mcbond_it	0.648
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6556
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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.