Experiment: 4U82

Structure of S. aureus undecaprenyl diphosphate synthase in complex with FSPP and sulfate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		298	100 mM MES sodium, pH 6.5, 200 mM ammonium sulfate, 25% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.079	α = 90
b = 57.079	β = 90
c = 158.618	γ = 90

Symmetry
Space Group	P 41 21 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 300 mm CCD		2012-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	1.66	50	99.5	0.068	34.5714	14.3		32040

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)
	1.66	1.69			0.703	4.5714	14.3

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	4H8E	1.66	46.33	31968	1616	99.98	0.1889	0.1873	0.1899	0.2198	0.2186	RANDOM	20.106

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.881
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	14.386
r_dihedral_angle_1_deg	6.552
r_angle_refined_deg	2.423
r_chiral_restr	0.176
r_bond_refined_d	0.026
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1930
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction