6MFU | pdb_00006mfu

Crystal structure of a Guanylate kinase from Cryptococcus neoformans var. grubii serotype A in complex with GDP and ADP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	285	Microlytic MCSG1 screen, C4: 25.5% PEG 3350, 170mM Ammonium Acetate, 15% glycerol, 100mM Ammonium acetate/HCl pH 4.6: CrneC.00217.a.B1.PW38472 at 15.5mg/ml + 4mM ADP + 4mM GDP + 4mM MgCl2: cryo: direct: tray 301682c4, puck xcr5-9: for phasing a crystal from the same drop was incubated for 20sec each in reservoir + compounds + 5% 5M NaI in EG and 10% 5M NaI in EG, and directly vitrified, puck: TDC2-4

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.67	α = 90
b = 99.15	β = 91.23
c = 90.05	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		2018-09-01	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2018-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97741	ALS	5.0.1
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.6	49.575	96.7	0.021	0.025	1	30.65	3.253		131080			27.655

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	89.6		0.201	0.247	0.948	4.4	2.597

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	1.6	49.575	1.35	131039	1905	96.72	0.1498	0.1494	0.15	0.1755	0.18	0	25.0433

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
f_dihedral_angle_d	13.408
f_angle_d	0.978
f_chiral_restr	0.054
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6701
Nucleic Acid Atoms
Solvent Atoms	1248
Heterogen Atoms	204

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
ARP/wARP	model building
Coot	model building

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.