3T55 | pdb_00003t55

Crystal structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in complex with Phenoxymethyl Benzoic Acid (PMBA)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	0.1M Sodium acetate trihydrate, 2.0 ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.838	α = 90
b = 53.206	β = 90
c = 87.167	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	ADSC QUANTUM 315	mirrors	2009-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97711	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.06	50	99.9	0.118	0.118	11.7	8.2	13524	13524			18.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.06	2.14	99.7		0.425	0.425	9.2	8.5	657

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1IGS	2.06	40.57	13451	13451	677	98.48	0.1878	0.1878	0.1847	0.19	0.2495	0.25	RANDOM	24.0498

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]
0.18			0.01		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.214
r_dihedral_angle_4_deg	15.328
r_dihedral_angle_3_deg	14.133
r_dihedral_angle_1_deg	5.603
r_scangle_it	4.41
r_scbond_it	2.746
r_angle_refined_deg	1.759
r_mcangle_it	1.689
r_angle_other_deg	1.032
r_mcbond_it	0.982

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.214
r_dihedral_angle_4_deg	15.328
r_dihedral_angle_3_deg	14.133
r_dihedral_angle_1_deg	5.603
r_scangle_it	4.41
r_scbond_it	2.746
r_angle_refined_deg	1.759
r_mcangle_it	1.689
r_angle_other_deg	1.032
r_mcbond_it	0.982
r_mcbond_other	0.284
r_chiral_restr	0.101
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1838
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	29

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.