3TQ3 | pdb_00003tq3

Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D4L	PDB entry 2D4L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.594	α = 90
b = 60.594	β = 90
c = 64.146	γ = 120

Symmetry
Space Group	P 63

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	MAR CCD 165 mm	mirrors	2003-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8124	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.85	52.49	99.8	0.078	20.2	11.2	11478	11478		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.96	99.7		0.539	5	11.2	1821

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	rigid body refinement	THROUGHOUT	PDB entry 2D4L	1.85	20	11477	10863	614	99.84	0.1546	0.1538	0.16	0.1688	0.17	RANDOM	25.398

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]
0.67	0.33		0.67		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.671
r_dihedral_angle_4_deg	29.618
r_dihedral_angle_3_deg	12.472
r_dihedral_angle_1_deg	6.456
r_scangle_it	3.958
r_scbond_it	2.715
r_angle_refined_deg	1.812
r_mcangle_it	1.751
r_mcbond_it	1.115
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.671
r_dihedral_angle_4_deg	29.618
r_dihedral_angle_3_deg	12.472
r_dihedral_angle_1_deg	6.456
r_scangle_it	3.958
r_scbond_it	2.715
r_angle_refined_deg	1.812
r_mcangle_it	1.751
r_mcbond_it	1.115
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.203
r_symmetry_hbond_refined	0.168
r_chiral_restr	0.129
r_metal_ion_refined	0.059
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	825
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
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.