5QPQ | pdb_00005qpq

PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000631a

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
2.32	46.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.912	α = 90
b = 57.912	β = 90
c = 396.13	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		2017-10-07		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	1.49	198.08	99.8	0.082	0.084	0.02	0.998	16.2	16.7		66315

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	1.49	1.53	98.1		2.045	2.137	0.612	0.534		12	4670

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	1.49	66.02	61689	3370	98.06	0.2013	0.1995	0.21	0.2347	0.24	RANDOM	26.65

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]
0.13	0.06		0.13		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.821
r_dihedral_angle_4_deg	16.731
r_dihedral_angle_3_deg	15.151
r_dihedral_angle_1_deg	5.538
r_mcangle_it	3.349
r_angle_refined_deg	2.411
r_mcbond_it	2.393
r_mcbond_other	2.393
r_angle_other_deg	1.174
r_chiral_restr	0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.821
r_dihedral_angle_4_deg	16.731
r_dihedral_angle_3_deg	15.151
r_dihedral_angle_1_deg	5.538
r_mcangle_it	3.349
r_angle_refined_deg	2.411
r_mcbond_it	2.393
r_mcbond_other	2.393
r_angle_other_deg	1.174
r_chiral_restr	0.15
r_bond_refined_d	0.027
r_gen_planes_refined	0.013
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	335
Heterogen Atoms	30

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.