3TPY | pdb_00003tpy

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
2.09	41.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.559	α = 90
b = 60.559	β = 90
c = 63.635	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	2003-02-09	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2003-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8028	EMBL/DESY, HAMBURG	X13
2	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0720	ESRF	ID14-4

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
1,2	1.75	20	99.8	0.032	44.8	11.4	13399	13399		-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)
1,2	1.75	1.77	100		0.402	4.4	11.3	438

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	SIRAS	THROUGHOUT	PDB entry 2D4L	1.75	20	13305	12600	705	99.03	0.1536	0.1517	0.15	0.1864	0.19	RANDOM	27.004

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]
0.79	0.4		0.79		-1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.517
r_dihedral_angle_4_deg	28.651
r_dihedral_angle_3_deg	15.274
r_scangle_it	9.959
r_scbond_it	6.941
r_dihedral_angle_1_deg	5.745
r_mcangle_it	3.509
r_mcbond_it	2.722
r_angle_refined_deg	1.957
r_nbtor_refined	0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.517
r_dihedral_angle_4_deg	28.651
r_dihedral_angle_3_deg	15.274
r_scangle_it	9.959
r_scbond_it	6.941
r_dihedral_angle_1_deg	5.745
r_mcangle_it	3.509
r_mcbond_it	2.722
r_angle_refined_deg	1.957
r_nbtor_refined	0.325
r_symmetry_vdw_refined	0.261
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.17
r_chiral_restr	0.118
r_metal_ion_refined	0.099
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	831
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	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.