9P5I | pdb_00009p5i

E. coli Dihydropteroate Synthase in complex with pterin-based inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5U10

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	50 mM Tris, 32-50% Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.721	α = 90
b = 94.551	β = 90
c = 136.846	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	CCD	MARMOSAIC 225 mm CCD		2021-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.14	68.42	98.2	0.12	0.131	0.051	0.998	18.1	11.8		31532			25.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.2	91.3		0.626	0.771	0.443	0.722	2.4	5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.141	68.42	31477	1490	97.983	0.194	0.1921	0.1921	0.238	0.2379	RANDOM	28.506

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]
-0.849			-0.511		1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.954
r_dihedral_angle_3_deg	12.617
r_lrange_it	6.668
r_dihedral_angle_1_deg	6.124
r_dihedral_angle_2_deg	5.337
r_scangle_it	5.234
r_mcangle_it	3.642
r_scbond_it	3.619
r_mcbond_it	2.46
r_angle_refined_deg	1.626
r_nbtor_refined	0.304
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.172
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.104
r_ncsr_local_group_1	0.096
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3885
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	42

Software

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