2WGD | pdb_00002wgd

Crystal structure of KasA of Mycobacterium tuberculosis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GP6	PDB ENTRY 2GP6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				2-PROPANOL, NACL HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.529	α = 90
b = 77.529	β = 90
c = 146.803	γ = 120

Symmetry
Space Group	P 31 2 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		RIGAKU IMAGING PLATE			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	2.01	39.55	99.7	0.08	9	4.4		34607			25.4

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	2.01	2.08	100		0.34	3	4.3

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 (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 2GP6	2.01	38.778	34601	1734	99.594	0.181	0.1798	0.19	0.2143	0.22	RANDOM	32.865

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]
0.947	0.474		0.947		-1.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.678
r_dihedral_angle_4_deg	16.801
r_dihedral_angle_3_deg	11.889
r_dihedral_angle_1_deg	5.959
r_scangle_it	3.264
r_scbond_it	1.952
r_angle_refined_deg	1.296
r_mcangle_it	1.245
r_mcbond_it	0.666
r_symmetry_vdw_other	0.304
r_nbd_refined	0.219
r_nbtor_refined	0.17
r_symmetry_hbond_refined	0.139
r_mcbond_other	0.138
r_xyhbond_nbd_refined	0.127
r_symmetry_vdw_refined	0.125
r_metal_ion_refined	0.107
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
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	3029
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing