3IIB | pdb_00003iib

Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.2000M MgCl2, 30.0000% PEG-400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.442	α = 90
b = 84.867	β = 115.85
c = 80.114	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-04-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97791	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	29.374	97.4	0.12	0.12	7.9	2.6		58230			10.978

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	96		0.462	0.462	1.9	2.6	4239

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	MAD	THROUGHOUT	1.7	29.374	58229	2960	97.26	0.152	0.151	0.16	0.182	0.19	RANDOM	11.122

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]
0.06		-0.34	-0.17		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.001
r_dihedral_angle_4_deg	19.14
r_dihedral_angle_3_deg	11.636
r_dihedral_angle_1_deg	6.448
r_scangle_it	6.271
r_scbond_it	4.048
r_mcangle_it	2.466
r_mcbond_it	1.64
r_angle_refined_deg	1.471
r_angle_other_deg	0.909

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.001
r_dihedral_angle_4_deg	19.14
r_dihedral_angle_3_deg	11.636
r_dihedral_angle_1_deg	6.448
r_scangle_it	6.271
r_scbond_it	4.048
r_mcangle_it	2.466
r_mcbond_it	1.64
r_angle_refined_deg	1.471
r_angle_other_deg	0.909
r_mcbond_other	0.53
r_chiral_restr	0.087
r_bond_refined_d	0.017
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	3283
Nucleic Acid Atoms
Solvent Atoms	631
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHARP	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.