5NNH | pdb_00005nnh

KSHV uracil-DNA glycosylase, apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J8X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.1 M bis-tris, 0.2 M lithium sulfate monohydrate, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.201	α = 90
b = 53.811	β = 93.39
c = 40.811	γ = 90

Symmetry
Space Group	C 1 2 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		2017-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96858	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	52.63	100	0.089	0.204	0.996	8.2	16.1		11700

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	100		0.567	0.858		15

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	MOLECULAR REPLACEMENT	THROUGHOUT	2J8X	2.2	52.51	11642	442	99.51	0.196	0.194	0.1986	0.2436	0.2497	RANDOM	50.2919

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]
-0.83		-0.03	1.73		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.895
r_dihedral_angle_4_deg	20.491
r_dihedral_angle_3_deg	15.049
r_dihedral_angle_1_deg	6.671
r_angle_other_deg	3.825
r_mcangle_it	1.996
r_angle_refined_deg	1.606
r_mcbond_it	1.159
r_mcbond_other	1.158
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_other	0.008
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1740
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement