1VLH | pdb_00001vlh

Crystal structure of Phosphopantetheine adenylyltransferase (TM0741) from Thermotoga maritima at 2.20 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B6T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	277	0.2M MgCl2, 35.0% MPD, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	46.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.963	α = 90
b = 110.876	β = 111.98
c = 74.087	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		2003-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	68.7	94.5	0.046	14.5	3.1		48776			47.96

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	68		0.468	2	1.9	2564

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	1b6t	2.2	68.7	46254	2497	94.36	0.17332	0.17051	0.18	0.22687	0.23	RANDOM	41.497

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]
-1.92		-1.41	-1.44		2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.939
r_dihedral_angle_4_deg	20.308
r_dihedral_angle_3_deg	18.255
r_dihedral_angle_1_deg	7.716
r_scangle_it	7.412
r_scbond_it	5.857
r_mcangle_it	2.681
r_mcbond_it	1.835
r_angle_refined_deg	1.716
r_angle_other_deg	0.9
r_mcbond_other	0.493
r_symmetry_vdw_other	0.274
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.206
r_nbd_other	0.184
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.096
r_nbtor_other	0.092
r_xyhbond_nbd_other	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7520
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	140

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling