3H2M | pdb_00003h2m

Structural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TX0	PDB entry 1TX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	291	LITHIUM SULFATE, propane, Bis-Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.155	α = 90
b = 99.155	β = 90
c = 262.077	γ = 120

Symmetry
Space Group	P 62 2 2

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	MARRESEARCH		2008-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	2.31	44.74	89.8	0.113	26.5	10.5		30988

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	2.31	2.38	56.2		0.326	4.6	6	1881

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	PDB entry 1TX0	2.31	44.74	30942	1567	89.84	0.20589	0.20283	0.2	0.26548	0.26	RANDOM	64.685

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]
3.81	1.9		3.81		-5.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.669
r_dihedral_angle_4_deg	20.951
r_dihedral_angle_3_deg	16.975
r_dihedral_angle_1_deg	6.455
r_scangle_it	4.8
r_scbond_it	3.134
r_angle_refined_deg	1.97
r_mcangle_it	1.765
r_mcbond_it	1.135
r_symmetry_vdw_refined	0.328
r_nbtor_refined	0.31
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.204
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.129
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4087
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	86

Software

Software
Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling