5QP2 | pdb_00005qp2

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z1170065264

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	50.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.811	α = 90
b = 60.694	β = 90
c = 65.267	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	1.83	28.74	99.8	0.039	0.042	0.017	1	22.9	6.4		17302

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	1.83	1.88	98.9		0.824	0.894	0.341	0.916		6.6	1237

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	1.83	44.49	16429	831	99.75	0.1956	0.1931	0.21	0.2501	0.26	RANDOM	45.942

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]
3.53			-3.36		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.35
r_dihedral_angle_4_deg	21.351
r_dihedral_angle_3_deg	16.237
r_dihedral_angle_1_deg	6.826
r_mcangle_it	5.729
r_mcbond_it	3.849
r_mcbond_other	3.847
r_angle_refined_deg	1.87
r_angle_other_deg	1.108
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.35
r_dihedral_angle_4_deg	21.351
r_dihedral_angle_3_deg	16.237
r_dihedral_angle_1_deg	6.826
r_mcangle_it	5.729
r_mcbond_it	3.849
r_mcbond_other	3.847
r_angle_refined_deg	1.87
r_angle_other_deg	1.108
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1195
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	39

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.