4RFV | pdb_00004rfv

Structure of the Mycobacterium tuberculosis APS kinase CysC Cys556Ala mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BZP	PDB entry 4BZP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	21% PEG 3350, 0.2M ammonium nitrate, 5mM magnesium chloride, 5mM ADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.167	α = 90
b = 71.158	β = 90
c = 118.56	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	PSI PILATUS 6M	mirrors	2014-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91842	BESSY	14.1

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	1.69	59.28	99.9	0.063	0.063	13.9	5.9	32714	32681	3	3	16.8

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	1.69	1.72	99.1		0.47	0.47	3	6	1620

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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 4BZP	1.69	59.28	3	31032	31032	1606	99.97	0.18619	0.18427	0.19	0.22275	0.23	RANDOM	24.155

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]
0.47			0.28		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.531
r_dihedral_angle_3_deg	13.933
r_dihedral_angle_4_deg	12.573
r_long_range_B_refined	6.563
r_long_range_B_other	6.306
r_dihedral_angle_1_deg	5.11
r_scangle_other	4.177
r_mcangle_it	2.801
r_mcangle_other	2.8
r_scbond_it	2.688
r_scbond_other	2.663
r_mcbond_it	1.849
r_mcbond_other	1.846
r_angle_refined_deg	1.548
r_angle_other_deg	0.8
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2190
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	5

Software

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