3OIS | pdb_00003ois

Crystal Structure Xylellain, a cysteine protease from Xylella fastidiosa

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	20-22% PEG 4000, 60 mM Sodium citrate, 134 mM Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.089	α = 75.86
b = 69.314	β = 75.43
c = 82.368	γ = 66.51

Symmetry
Space Group	P 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	IMAGE PLATE	MAR scanner 345 mm plate	MIRROR	2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

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	1.65	78.664	91	0.054	0.054	27	8.1	117070	117070	2	2

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	1.65	1.74	86.7		0.4	0.4	1.9	4.4	16308

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.65	23.06	116835	116835	5859	90.98	0.1685	0.1685	0.166	0.16	0.2159	0.21	RANDOM	22.8106

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]
0.62	1.31	-0.05	-0.82	-0.1	-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.169
r_dihedral_angle_4_deg	20.555
r_dihedral_angle_3_deg	14.671
r_dihedral_angle_1_deg	6.246
r_scangle_it	4.483
r_scbond_it	3.095
r_angle_refined_deg	2.089
r_mcangle_it	2.021
r_mcbond_it	1.303
r_chiral_restr	0.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.169
r_dihedral_angle_4_deg	20.555
r_dihedral_angle_3_deg	14.671
r_dihedral_angle_1_deg	6.246
r_scangle_it	4.483
r_scbond_it	3.095
r_angle_refined_deg	2.089
r_mcangle_it	2.021
r_mcbond_it	1.303
r_chiral_restr	0.146
r_bond_refined_d	0.026
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8578
Nucleic Acid Atoms
Solvent Atoms	1435
Heterogen Atoms	100

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

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.