4HLB

Crystal structure of an alpha-lytic protease prodomain-like protein (DESPIG_01740) from Desulfovibrio piger ATCC 29098 at 1.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.20M sodium acetate, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.821	α = 90
b = 57.821	β = 90
c = 63.89	γ = 120

Symmetry
Space Group	P 32 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	ADSC QUANTUM 315	KOHZU: Double Crystal Si(111)	2012-09-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.979095,0.979338,0.953725	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	28.91	100	0.103	16.3	13.3	11856	11856			26.12

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	1.8	1.85	100		0.014	1.374	0.6	8	843

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	28.91	11834	562	99.97	0.1966	0.1953	0.2228	RANDOM	33.7023

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]
0.49	0.49		0.49		-1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.821
r_dihedral_angle_4_deg	18.443
r_dihedral_angle_3_deg	13.99
r_dihedral_angle_1_deg	5.462
r_angle_refined_deg	1.361
r_angle_other_deg	0.732
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.821
r_dihedral_angle_4_deg	18.443
r_dihedral_angle_3_deg	13.99
r_dihedral_angle_1_deg	5.462
r_angle_refined_deg	1.361
r_angle_other_deg	0.732
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	751
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.