5QQ8 | pdb_00005qq8

PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOOA000563a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	80 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.781	α = 90
b = 57.781	β = 90
c = 396.935	γ = 120

Symmetry
Space Group	P 61 2 2

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-F		2017-10-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.62	132.37	100	0.136	0.14	0.033	0.999	10.8	17.6		52032

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	1.62	1.66	100		2.343	2.426	0.624	0.536		14.9	3734

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	FOURIER SYNTHESIS	THROUGHOUT	1YHK	1.62	66.16	48732	2657	98.93	0.1996	0.1976	0.21	0.2351	0.24	RANDOM	28.26

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]
0.17	0.08		0.17		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.328
r_dihedral_angle_4_deg	17.226
r_dihedral_angle_3_deg	14.329
r_dihedral_angle_1_deg	5.409
r_mcangle_it	3.727
r_mcbond_other	2.77
r_mcbond_it	2.769
r_angle_refined_deg	2.095
r_angle_other_deg	1.159
r_chiral_restr	0.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.328
r_dihedral_angle_4_deg	17.226
r_dihedral_angle_3_deg	14.329
r_dihedral_angle_1_deg	5.409
r_mcangle_it	3.727
r_mcbond_other	2.77
r_mcbond_it	2.769
r_angle_refined_deg	2.095
r_angle_other_deg	1.159
r_chiral_restr	0.143
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2871
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

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.