5ETP | pdb_00005etp

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.05 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q0N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.1	281	PROTEIN 6.6 MG/ML 1 MM AMPCPP, 1 MM INHIBITOR, 2 MM MAGNESIUM CHLORIDE, 20%w/v PEG4000, 0.1 M TRIS CHLORIDE, 0.172 M CALCIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.95	α = 90
b = 57.77	β = 116.11
c = 38.64	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 QUANTUM 315r		2015-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9707	Australian Synchrotron	MX2

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	1.05	34.7	99.8	0.087	13.4	7.1		66451

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	1.05	1.06	99.2		0.298	5.1	6.5

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	1Q0N	1.05	34.7	63260	3162	99.72	0.10791	0.10706	0.11	0.12504	0.13	RANDOM	6.66

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]
-0.07		0.05	0.06		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.606
r_sphericity_free	20.21
r_dihedral_angle_4_deg	16.169
r_rigid_bond_restr	12.398
r_dihedral_angle_3_deg	10.271
r_dihedral_angle_1_deg	6.346
r_sphericity_bonded	4.797
r_angle_other_deg	3.529
r_long_range_B_refined	2.407
r_long_range_B_other	2.406
r_angle_refined_deg	2.099
r_scangle_other	1.196
r_scbond_it	0.931
r_scbond_other	0.931
r_mcangle_it	0.829
r_mcangle_other	0.829
r_mcbond_it	0.625
r_mcbond_other	0.625
r_chiral_restr	0.116
r_gen_planes_other	0.022
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1280
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
XDS	data reduction
Coot	model building