4PS6 | pdb_00004ps6

Crystal structure of an inhibitor of vertebrate lysozyme (PA3902) from Pseudomonas aeruginosa PAO1 at 1.25 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	0.2M ammonium acetate, 30.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.449	α = 90
b = 47.057	β = 96.91
c = 36.389	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2013-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		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	1.25	36.126	84.9	0.073	15.57			26432		-3	9.938

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	1.25	1.29	23.4		0.613	1.7

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	SAD	THROUGHOUT	1.25	36.126	26429	1326	85.84	0.1185	0.1161	0.13	0.1639	0.17	RANDOM	14.0087

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		0.1	0.21		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	30.03
r_dihedral_angle_2_deg	29.233
r_dihedral_angle_3_deg	10.705
r_dihedral_angle_4_deg	9.421
r_sphericity_bonded	8.731
r_dihedral_angle_1_deg	5.517
r_mcangle_it	1.611
r_rigid_bond_restr	1.464
r_angle_refined_deg	1.317
r_mcbond_it	1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	30.03
r_dihedral_angle_2_deg	29.233
r_dihedral_angle_3_deg	10.705
r_dihedral_angle_4_deg	9.421
r_sphericity_bonded	8.731
r_dihedral_angle_1_deg	5.517
r_mcangle_it	1.611
r_rigid_bond_restr	1.464
r_angle_refined_deg	1.317
r_mcbond_it	1.27
r_mcbond_other	1.27
r_angle_other_deg	0.759
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1023
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms

Software

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