3SH0

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1065

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E98	pdb entry 2E98

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	50mM HEPES, pH 7.5, 5% PEG 4,000, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.765	α = 90
b = 68.724	β = 90
c = 112.056	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARMOSAIC 300 mm CCD		2010-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9787	APS	21-ID-D

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	1.84	50	99.3	0.065	8.1	10		42560	1	1

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	1.84	1.87	89.2		0.642		5.3	1870

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2E98	1.84	35.71	44483	42354	2129	98.96	0.1704	0.1704	0.1683	0.2111	RANDOM	30.229

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			-0.07		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.569
r_dihedral_angle_4_deg	19.616
r_dihedral_angle_3_deg	14.541
r_dihedral_angle_1_deg	5.649
r_scangle_it	5.185
r_scbond_it	3.318
r_mcangle_it	2.049
r_angle_refined_deg	1.901
r_mcbond_it	1.231
r_chiral_restr	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.569
r_dihedral_angle_4_deg	19.616
r_dihedral_angle_3_deg	14.541
r_dihedral_angle_1_deg	5.649
r_scangle_it	5.185
r_scbond_it	3.318
r_mcangle_it	2.049
r_angle_refined_deg	1.901
r_mcbond_it	1.231
r_chiral_restr	0.16
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3397
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	69

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
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.