4QYB | pdb_00004qyb

2.1 Angstrom resolution crystal structure of uncharacterized protein, disulfide-bridged dimer, from Burkholderia cenocepacia J2315

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PUP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	protein - 9.6 mg/mL in 10 mM Tris-HCl pH 8.3, 250 mM NaCl, 5 mM BME, crystallization - The Classics II Suite C4 (28): 560 mM Sodium citrate pH 7.0, cryo - 25% (v/v) sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.945	α = 90
b = 85.634	β = 90
c = 93.669	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	MARMOSAIC 225 mm CCD	Be lenses	2014-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	30	95.1	0.063	49.5	7.2	14651	14651		-3	40.5

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	2.14	100		0.41	5.3	7.4	746

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	4PUP	2.1	28.9	13578	13578	717	92.1	0.21315	0.21094	0.22	0.25648	0.26	RANDOM	54.647

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]
0.78			5.23		-6.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.586
r_dihedral_angle_3_deg	14.608
r_dihedral_angle_4_deg	11.593
r_dihedral_angle_1_deg	3.56
r_angle_refined_deg	1.569
r_angle_other_deg	0.977
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.586
r_dihedral_angle_3_deg	14.608
r_dihedral_angle_4_deg	11.593
r_dihedral_angle_1_deg	3.56
r_angle_refined_deg	1.569
r_angle_other_deg	0.977
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1727
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.