4QCA | pdb_00004qca

Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant R167AD4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DOF	PDB ENTRY 4DOF, CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	277	2:1:1 protein solution/water/reservoir (unbuffered 16% PEG3350, 0.15 M potassium fluoride, 10% glycerol), pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.14	α = 90
b = 118.268	β = 90
c = 121.97	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	100	PIXEL	DECTRIS PILATUS 6M	Mirrors	2012-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97920	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	46.57	97.4	0.11	0.11	13.4	7.7	80549	80549			22.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	97.6		0.597	0.597	3.9	8.1	11684

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 (All)	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	PDB ENTRY 4DOF, CHAIN A	1.9	42.45	80488	80488	4036	97.16	0.206	0.206	0.2044	0.2103	0.2358	0.2423	RANDOM	24.52

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.767
r_dihedral_angle_4_deg	10.999
r_dihedral_angle_3_deg	10.783
r_dihedral_angle_1_deg	5.819
r_mcangle_it	1.672
r_angle_refined_deg	1.113
r_mcbond_it	0.981
r_mcbond_other	0.981
r_angle_other_deg	0.757
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7111
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
RAPD	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing