3KD4

CRYSTAL STRUCTURE OF A PUTATIVE PROTEASE (BDI_1141) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.00 A RESOLUTION

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.67	277	25.0000% Glycerol, 1.1000M ammonium dihydrogen phosphate, 0.1M citric acid pH 5.67, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.28	71.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.167	α = 90
b = 159.397	β = 91.64
c = 78.23	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)	2009-06-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97913,0.97860	SSRL	BL11-1

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	28.928	96.9	0.085	7.59			125591		-3	25.142

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	2.07	95.9		0.559	1.6

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	2	28.928	125591	6308	99.57	0.172	0.17	0.2	RANDOM	25.486

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]
1.08		0.1	-0.18		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.937
r_dihedral_angle_4_deg	20.192
r_dihedral_angle_3_deg	12.53
r_dihedral_angle_1_deg	6.006
r_scangle_it	4.191
r_scbond_it	2.516
r_mcangle_it	1.561
r_angle_refined_deg	1.523
r_angle_other_deg	0.883
r_mcbond_it	0.839

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.937
r_dihedral_angle_4_deg	20.192
r_dihedral_angle_3_deg	12.53
r_dihedral_angle_1_deg	6.006
r_scangle_it	4.191
r_scbond_it	2.516
r_mcangle_it	1.561
r_angle_refined_deg	1.523
r_angle_other_deg	0.883
r_mcbond_it	0.839
r_mcbond_other	0.208
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7696
Nucleic Acid Atoms
Solvent Atoms	1095
Heterogen Atoms	156

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

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.