5QOZ | pdb_00005qoz

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with PB1787571279

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.1 M acetate, pH 4.5, 5-25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.125	α = 90
b = 60.472	β = 90
c = 64.951	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	DECTRIS PILATUS 2M		2017-07-27		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	1.7	28.61	99.5	0.081	0.088	0.035	0.996	13.7	6.3		21501

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	1.7	1.74	97.7		0.854	0.948	0.405	0.756		5.3	1540

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	PDB entry 5MP0	1.7	44.3	20408	1045	99.35	0.2194	0.2167	0.23	0.275	0.28	RANDOM	31.623

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]
1.09			-1.89		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.104
r_dihedral_angle_4_deg	26.045
r_dihedral_angle_3_deg	15.565
r_dihedral_angle_1_deg	7.941
r_mcangle_it	4.351
r_mcbond_it	3.008
r_mcbond_other	3.002
r_angle_refined_deg	2.091
r_angle_other_deg	1.145
r_chiral_restr	0.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.104
r_dihedral_angle_4_deg	26.045
r_dihedral_angle_3_deg	15.565
r_dihedral_angle_1_deg	7.941
r_mcangle_it	4.351
r_mcbond_it	3.008
r_mcbond_other	3.002
r_angle_refined_deg	2.091
r_angle_other_deg	1.145
r_chiral_restr	0.133
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1189
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	36

Software

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