4CKW

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y71	PDB ENTRY 2Y71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		12% GLYCEROL, 1.5 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.386	α = 90
b = 94.294	β = 97.28
c = 61.354	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)	2013-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC		ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	94.29	99	0.1	10.8	3.4		11546		-3	33.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	99.7		0.37	3.6	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Y71	2.7	60.86	10980	549	98.87	0.20525	0.20031	0.30452	RANDOM	36.218

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]
0.99		-0.58	-0.74		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.815
r_dihedral_angle_4_deg	20.004
r_dihedral_angle_3_deg	15.333
r_dihedral_angle_1_deg	6.722
r_scbond_it	5
r_mcangle_it	2.968
r_mcbond_it	1.699
r_scangle_it	1.339
r_angle_refined_deg	1.182
r_angle_other_deg	0.711
r_mcbond_other	0.247
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.212
r_symmetry_vdw_other	0.189
r_xyhbond_nbd_refined	0.183
r_nbd_other	0.168
r_nbtor_refined	0.166
r_symmetry_hbond_refined	0.15
r_nbtor_other	0.082
r_chiral_restr	0.058
r_xyhbond_nbd_other	0.015
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3427
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALE	data scaling
PHASER	phasing