3NPD | pdb_00003npd

Crystal structure of a putative secreted protein (PA3611) from PSEUDOMONAS AERUGINOSA at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	2.000000000M (NH4)2SO4, 0.200000000M Li2SO4, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.989	α = 90
b = 51.317	β = 90
c = 56.898	γ = 90

Symmetry
Space Group	P 21 21 21

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		2010-05-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97941,0.97925	SSRL	BL9-2

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	1.6	28.909	98.5	0.06	7.97			14032		-3	17.794

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	1.6	1.66	96.1		0.473	1.5

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	MAD	THROUGHOUT	1.6	28.909	13997	700	99.53	0.1623	0.1602	0.17	0.2046	0.21	RANDOM	22.6714

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]
-1.49			0.29		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.205
r_dihedral_angle_4_deg	16.09
r_dihedral_angle_3_deg	12.195
r_scangle_it	8.324
r_scbond_it	5.402
r_dihedral_angle_1_deg	4.978
r_mcangle_it	2.988
r_mcbond_it	1.798
r_angle_refined_deg	1.696
r_angle_other_deg	1.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.205
r_dihedral_angle_4_deg	16.09
r_dihedral_angle_3_deg	12.195
r_scangle_it	8.324
r_scbond_it	5.402
r_dihedral_angle_1_deg	4.978
r_mcangle_it	2.988
r_mcbond_it	1.798
r_angle_refined_deg	1.696
r_angle_other_deg	1.305
r_mcbond_other	0.557
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	868
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	69

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

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.