1Z8F | pdb_00001z8f

Guanylate Kinase Double Mutant A58C, T157C from Mycobacterium tuberculosis (Rv1389)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S4Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	2.6M sodium formate, 2% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.306	α = 90
b = 112.306	β = 90
c = 112.306	γ = 90

Symmetry
Space Group	I 2 3

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	ADSC QUANTUM 315		2004-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	90	100	0.042	35.6	10.9	8301	8301

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	100		0.446	5.8	10.3	807

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Difference Fourier Map	THROUGHOUT	1S4Q	2.5	79.31	7909	7909	375	99.78	0.18314	0.18314	0.18061	0.18	0.23576	0.23	RANDOM	46.517

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.58
r_dihedral_angle_4_deg	18.077
r_dihedral_angle_3_deg	15.669
r_dihedral_angle_1_deg	5.207
r_scangle_it	4.691
r_scbond_it	2.732
r_mcangle_it	1.47
r_angle_refined_deg	1.444
r_mcbond_it	1.35
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.58
r_dihedral_angle_4_deg	18.077
r_dihedral_angle_3_deg	15.669
r_dihedral_angle_1_deg	5.207
r_scangle_it	4.691
r_scbond_it	2.732
r_mcangle_it	1.47
r_angle_refined_deg	1.444
r_mcbond_it	1.35
r_nbtor_refined	0.308
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.142
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1394
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.