3QJA

Crystal Structure of the Mycobacterium tuberculosis Indole-3-glycerol phosphate synthase (TrpC) in apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VC4	PDB entry 1VC4

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.069	α = 90
b = 53.505	β = 90
c = 87.826	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 300 mm CCD	mirrors	2009-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97933	APS	23-ID-D

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	1.29	50	99.9	0.067	0.067	15.6	13.8	59034	59034			12.6

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	1.29	1.31	100		0.424	0.424	9.54	12.8	2905

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VC4	1.29	33.45	58786	58786	2980	99.75	0.1641	0.1641	0.1632	0.1809	RANDOM	16.1591

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]
0.02					-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.697
r_dihedral_angle_4_deg	15.172
r_dihedral_angle_3_deg	11.13
r_dihedral_angle_1_deg	4.835
r_sphericity_free	3.079
r_scangle_it	2.709
r_scbond_it	1.8
r_rigid_bond_restr	1.729
r_sphericity_bonded	1.619
r_mcangle_it	1.225
r_angle_refined_deg	1.097
r_angle_other_deg	0.858
r_mcbond_it	0.764
r_mcbond_other	0.268
r_nbd_refined	0.218
r_symmetry_vdw_other	0.205
r_nbd_other	0.195
r_symmetry_vdw_refined	0.17
r_nbtor_refined	0.164
r_symmetry_hbond_refined	0.126
r_xyhbond_nbd_refined	0.103
r_nbtor_other	0.086
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1806
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	5

Software

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