4GIE | pdb_00004gie

Crystal structure of prostaglandin F synthase from Trypanosoma cruzi bound to NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FZI	PDB ENTRY 4FZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	TrcrA.00019.a.B1 at 20 mg/mL with 2 mM NADP against Index G6: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, cryoprotectant: 15% ethylene glycol, crystal tracking ID 235869g6, unique puck ID pzu9-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.54	α = 90
b = 50.34	β = 94.23
c = 37.6	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315r		2012-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.25	50	94.7	0.062	23.41	7.6	80172	75887		-3	12.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.28	81		0.369	5.29

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4FZI	1.25	29.87	75882	3826	94.66	0.1202	0.1193	0.12	0.1362	0.14	RANDOM	9.0386

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.643
r_sphericity_free	24.053
r_dihedral_angle_4_deg	20.604
r_dihedral_angle_3_deg	10.971
r_dihedral_angle_1_deg	5.851
r_sphericity_bonded	4.628
r_angle_refined_deg	1.448
r_rigid_bond_restr	1.389
r_angle_other_deg	0.794
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.643
r_sphericity_free	24.053
r_dihedral_angle_4_deg	20.604
r_dihedral_angle_3_deg	10.971
r_dihedral_angle_1_deg	5.851
r_sphericity_bonded	4.628
r_angle_refined_deg	1.448
r_rigid_bond_restr	1.389
r_angle_other_deg	0.794
r_chiral_restr	0.085
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2309
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	52

Software

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

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.