5QPY | pdb_00005qpy

PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000449a

X-RAY DIFFRACTION

---

Starting Model(s)

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

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	46.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.824	α = 90
b = 57.824	β = 90
c = 395.675	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	1.67	197.84	100	0.18	0.186	0.044	0.999	10.5	17.9		47553

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	1.67	1.71	100		2.838	2.934	0.738	0.654		15.5	3406

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	1.67	65.95	44692	2407	99.35	0.1959	0.1935	0.2044	0.2381	0.2471	RANDOM	22.115

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]
0.14	0.07		0.14		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.526
r_dihedral_angle_4_deg	19.976
r_dihedral_angle_3_deg	14.656
r_dihedral_angle_1_deg	5.226
r_mcangle_it	2.667
r_angle_refined_deg	1.967
r_mcbond_it	1.841
r_mcbond_other	1.84
r_angle_other_deg	1.096
r_chiral_restr	0.124
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
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	325
Heterogen Atoms	34

Software

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