3GFV | pdb_00003gfv

Crystal Structure of Petrobactin-binding Protein YclQ from Bacillu subtilis

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	291	0.1 M Phosphate-citrate pH 4.2 40 %v/v PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.602	α = 90
b = 35.15	β = 91.53
c = 95.433	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	CCD	ADSC QUANTUM 315	mirrors	2008-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793	APS	19-ID

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	1.75	41.29	99.3	0.081	10.9	4.2	55926	55926			26.05

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)
	1.75	1.78	96.9		0.489	2.3	3.7	2667

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.75	41.286	1.34	55684	55684	2823	99.23	0.165	0.165	0.164	0.1636	0.191	0.1902	random

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]
0.2262		0.0577	5.1325		-5.3587

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.3
f_angle_deg	1.149
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4522
Nucleic Acid Atoms
Solvent Atoms	509
Heterogen Atoms	13

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing