3IVL | pdb_00003ivl

The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	297	40% PEG 300, 0.1M Sodium cacodylate pH 6.5, 0.2M Calcium acetate, vapor diffusion, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.173	α = 90
b = 108.173	β = 90
c = 113.995	γ = 120

Symmetry
Space Group	H 3

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		2009-07-14		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	2.1	50	99.6	0.099	10.3	4.4		28929

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	2.1	2.18	100		0.72		4.4	2896

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		THROUGHOUT	2.2	43.33	25100	1273	99.53	0.219	0.216	0.2307	0.258	0.2658	RANDOM	16.65

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]
-0.07	-0.03		-0.07		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.865
r_dihedral_angle_4_deg	20.679
r_dihedral_angle_3_deg	18.877
r_dihedral_angle_1_deg	5.628
r_scangle_it	2.712
r_scbond_it	1.84
r_angle_refined_deg	1.442
r_mcangle_it	0.936
r_mcbond_it	0.518
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.865
r_dihedral_angle_4_deg	20.679
r_dihedral_angle_3_deg	18.877
r_dihedral_angle_1_deg	5.628
r_scangle_it	2.712
r_scbond_it	1.84
r_angle_refined_deg	1.442
r_mcangle_it	0.936
r_mcbond_it	0.518
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2752
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	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.