1T6C | pdb_00001t6c

Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		A very incomplete model was obtained through experimental phasing and Arp/Warp tracing of the Type II crystal form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	293	MPD, MES, TRIS, KCl, DTT, The crystal was soaked in K2HgI4/KI containing solution, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.776	α = 90
b = 70.287	β = 90
c = 90.783	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	IMAGE PLATE	MARRESEARCH		2000-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	0.993	MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.53	15	95.8	0.069	0.061	22.8	6.9	47505	47505			19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.61	84.6		0.341	0.24	2.2	2.7	5936

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 (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 with partial model, followed by the Arp/Warp procedure.	THROUGHOUT	A very incomplete model was obtained through experimental phasing and Arp/Warp tracing of the Type II crystal form	1.53	15	47463	46991	472	95.6	0.162	0.162	0.17	0.217	0.22	RANDOM	16.249

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]
-0.88			-1		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.188
r_scangle_it	4.485
r_scbond_it	2.617
r_mcangle_it	1.698
r_angle_refined_deg	1.494
r_mcbond_it	0.879
r_angle_other_deg	0.85
r_symmetry_vdw_other	0.298
r_nbd_other	0.24
r_symmetry_hbond_refined	0.226
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.087
r_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2456
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing
ARP/wARP	model building