3ISF | pdb_00003isf

Structure of non-mineralized Bfrb (as-isolated) from Pseudomonas aeruginosa to 2.07A Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IS7	PDB entry 3IS7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	35% MPD, 100mM TRIS, 200mM ammonium sulfate, pH 8.5, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.761	α = 90
b = 126.274	β = 90
c = 168.553	γ = 90

Symmetry
Space Group	I 2 2 2

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 210r		2009-06-15		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	1.6531	APS	17-BM

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	2.07	44.02	99.5	0.09	0.09	20.279	6.9		79588		-3	31.3

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)
	2.07	2.14	97.8		0.504	0.504	2.375	5.3	7764

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3IS7	2.07	44.02	79324	3973	99.45	0.2	0.198	0.21	0.245	0.25	RANDOM	38.903

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]
2.07			-0.54		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.856
r_dihedral_angle_4_deg	29.273
r_dihedral_angle_3_deg	18.042
r_dihedral_angle_1_deg	5.265
r_scangle_it	4.624
r_scbond_it	2.952
r_angle_refined_deg	1.871
r_mcangle_it	1.645
r_mcbond_it	0.913
r_angle_other_deg	0.889

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.856
r_dihedral_angle_4_deg	29.273
r_dihedral_angle_3_deg	18.042
r_dihedral_angle_1_deg	5.265
r_scangle_it	4.624
r_scbond_it	2.952
r_angle_refined_deg	1.871
r_mcangle_it	1.645
r_mcbond_it	0.913
r_angle_other_deg	0.889
r_mcbond_other	0.277
r_chiral_restr	0.137
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7703
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	174

Software

Software
Software Name	Purpose
d*TREK	data scaling
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.