7NAA | pdb_00007naa

Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M06

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291.15	PEG 4000, Citrate buffer, Ammonium acetate pH 5.5, 10 mM Ikk16

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.127	α = 90
b = 239.33	β = 90
c = 53.982	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS3 6M		2019-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.75	39.9	99.41	0.145	0.159	0.065	0.99	11.14	5.8		34601

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.84	98.93		1.57	1.76	0.76	0.6	1.38

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	FREE R-VALUE	5m06	2.75	39.9	32914	1688	99.53	0.23888	0.2369	0.24	0.27887	0.28	RANDOM	64.4

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]
0.87			-2.11		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.238
r_dihedral_angle_4_deg	16.136
r_dihedral_angle_3_deg	14.057
r_dihedral_angle_1_deg	5.948
r_long_range_B_refined	5.13
r_long_range_B_other	5.111
r_mcangle_other	2.296
r_mcangle_it	2.295
r_scangle_other	2.181
r_angle_refined_deg	1.359
r_mcbond_it	1.33
r_mcbond_other	1.33
r_scbond_it	1.265
r_scbond_other	1.265
r_angle_other_deg	1.17
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6831
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	140

Software

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