Experiment: 3BSW

PglD-citrate complex, from Campylobacter jejuni NCTC 11168

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	SeMet derivative: 1 M sodium citrate, 100 mM imidazole, pH 8.0 in the resevior; protein solution containing 20 mM HEPES, 150 mM NaCl, pH 7.1, protein concentration of 10 mg/mL; drop made by mixing 1.5 uL of protein and resevoir solutions, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	4.2	277	Native: 20% PEG 1000, 100 mM phosphate-citrate, 200 mM Li2SO4, pH 4.2 in the resevior; protein solution containing 20 mM HEPES, 150 mM NaCl, pH 7.1, protein concentration of 10 mg/mL; drop made by mixing 1.5 uL of protein and resevoir solutions, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.347	α = 90
b = 86.347	β = 90
c = 65.538	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 210	Toroidal focusing mirror	2007-02-07	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.97840	NSLS	X6A

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	1.77	30	99.4	0.062	27.7	5.7	27293	27129			25.11

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)
	1.77	1.83	99.6		0.571	2.9	5.7	2695

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	1.77	30	27185	27106	1360	99.71	0.184	0.183	0.199	0.1966	RANDOM	25.892

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]
-0.04	-0.02		-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.81
r_dihedral_angle_3_deg	12.278
r_dihedral_angle_1_deg	5.865
r_dihedral_angle_4_deg	5.401
r_scangle_it	3.497
r_scbond_it	2.138
r_mcangle_it	1.291
r_angle_refined_deg	1.189
r_mcbond_it	0.697
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.81
r_dihedral_angle_3_deg	12.278
r_dihedral_angle_1_deg	5.865
r_dihedral_angle_4_deg	5.401
r_scangle_it	3.497
r_scbond_it	2.138
r_mcangle_it	1.291
r_angle_refined_deg	1.189
r_mcbond_it	0.697
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.225
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1397
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling