7CPN

CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	0.1 M citric acid sodium citrate pH 5.0, 0.7 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.095	α = 90
b = 137.878	β = 90
c = 168.652	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	100	CCD	ADSC QUANTUM 270		2009-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

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	2.28	47.534	100	0.059	63.647	8.4		77502

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	2.28	2.32	100		0.385	8.564	7.3

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1F75	2.28	47.534	76311	3830	99.877	0.205	0.2028	0.2394	53.909

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]
0.595			-0.417		-0.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.031
r_dihedral_angle_4_deg	17.237
r_dihedral_angle_3_deg	15.27
r_lrange_it	10.836
r_lrange_other	10.836
r_scangle_it	8.247
r_scangle_other	8.2
r_mcangle_other	7.009
r_mcangle_it	7.008
r_dihedral_angle_1_deg	5.784
r_scbond_it	5.464
r_scbond_other	5.374
r_mcbond_it	4.933
r_mcbond_other	4.928
r_angle_other_deg	2.309
r_angle_refined_deg	1.41
r_symmetry_nbd_refined	0.227
r_nbd_other	0.226
r_symmetry_nbd_other	0.216
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.07
r_bond_other_d	0.035
r_gen_planes_other	0.013
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11068
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing