7DNQ

Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GQU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	20% PEG 1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.1	α = 90
b = 112.1	β = 90
c = 112.1	γ = 90

Symmetry
Space Group	P 4 3 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	IMAGE PLATE	RIGAKU RAXIS IV++		2020-12-01	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	2.28	35	99.9	0.94	21.58	29.3		11541

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	2.28	2.36			0.66

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4GQU	2.28	28.041	11541	587	99.818	0.162	0.1591	0.2099	28.777

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.285
r_dihedral_angle_3_deg	16.027
r_dihedral_angle_4_deg	13.944
r_dihedral_angle_1_deg	7.34
r_lrange_it	5.774
r_lrange_other	5.731
r_scangle_it	4.379
r_scangle_other	4.377
r_mcangle_it	3.091
r_mcangle_other	3.09
r_scbond_it	2.826
r_scbond_other	2.824
r_mcbond_it	2.026
r_mcbond_other	2.022
r_angle_refined_deg	1.538
r_angle_other_deg	1.325
r_nbd_other	0.223
r_symmetry_nbd_refined	0.197
r_symmetry_nbd_other	0.195
r_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1459
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	17

Software

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