3U5W | pdb_00003u5w

Crystal Structure of a probable FAD-binding, putative uncharacterized protein from Brucella melitensis, apo form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	290	Internal tracking number 222033C10. JCSG screen condition C10: 10% PEG8000, 2% (v/v) dioxane, 0.1 M Bicine, BrabA.17620.a.A1 PS01056 at 40.2mg/ml, vapor diffusion, sitting drop, temperature 290K, pH 9.0, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.32	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.18	α = 90
b = 77.18	β = 90
c = 63.49	γ = 120

Symmetry
Space Group	P 32 2 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	CCD	RIGAKU SATURN 944+		2011-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541780

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	2.05	50	97.3	0.053	20.95	6.8		13680		-3	42.843

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	2.05	2.1	85.4		0.506	3.2	4.8

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 3UOI	2.05	50	13679	664	97.26	0.212	0.211	0.21	0.239	0.23	RANDOM	40.818

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]
0.05	0.03		0.05		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.446
r_dihedral_angle_3_deg	12.966
r_dihedral_angle_4_deg	10.697
r_dihedral_angle_1_deg	6.65
r_angle_refined_deg	1.363
r_angle_other_deg	0.799
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.446
r_dihedral_angle_3_deg	12.966
r_dihedral_angle_4_deg	10.697
r_dihedral_angle_1_deg	6.65
r_angle_refined_deg	1.363
r_angle_other_deg	0.799
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1004
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction
PHASER	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.