7DAH | pdb_00007dah

Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H3D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293.15	0.1M Morpheus Amino acids , 0.1M Morpheus Buffer System 3 , 30 % v/v Morpheus Precipitant Mix 3 (condition H11 of Morpheus screen from Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.603	α = 90
b = 136.603	β = 90
c = 121.931	γ = 120

Symmetry
Space Group	P 32

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	RIGAKU RAXIS IV++		2019-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.92	35	99.7	0.992	13	5.3		55130

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.92	3.02			0.497

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	1H3D	2.92	28.32	52562	2553	99.64	0.2186	0.2163	0.2155	0.2675	0.2639	RANDOM	64.28

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]
1.17	0.58		1.17		-3.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.768
r_dihedral_angle_4_deg	21.873
r_dihedral_angle_3_deg	20.649
r_dihedral_angle_1_deg	7.53
r_angle_refined_deg	1.773
r_angle_other_deg	1.329
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12785
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	176

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction