9PFL | pdb_00009pfl

Crystal structure of human 15-PGDH in complex with small molecule compound 1

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2M NaI, 0.1M Bis-Tris Propane, pH 6.5, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.695	α = 90
b = 107.234	β = 98.564
c = 47.027	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 PILATUS3 S 6M		2022-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.180730	CLSI	08B1-1

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	1.65	46.546	98.4	0.06	0.079	0.997	10.2	3.8		53999			17.239

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	1.65	1.68	99		0.408	0.535	0.821	2	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	46.546	53433	2680	97.356	0.193	0.1913	0.1908	0.2329	0.2334	24.289

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]
-0.528		0.117	-0.357		0.812

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.259
r_dihedral_angle_6_deg	15.223
r_dihedral_angle_3_deg	12.608
r_lrange_it	6.181
r_dihedral_angle_1_deg	5.955
r_scangle_it	4.897
r_scbond_it	3.251
r_mcangle_it	2.487
r_angle_refined_deg	1.785
r_mcbond_it	1.782

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.259
r_dihedral_angle_6_deg	15.223
r_dihedral_angle_3_deg	12.608
r_lrange_it	6.181
r_dihedral_angle_1_deg	5.955
r_scangle_it	4.897
r_scbond_it	3.251
r_mcangle_it	2.487
r_angle_refined_deg	1.785
r_mcbond_it	1.782
r_nbtor_refined	0.321
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.154
r_chiral_restr	0.117
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3892
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	196

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	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.