6YBH | pdb_00006ybh

Deoxyribonucleoside Kinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VP0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.1M KNa Tarta

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.929	α = 90
b = 190.929	β = 90
c = 115.461	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2019-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.4	42.66	99.78	0.799	40.13	14.8		61274

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.486			0.67

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	2VP0	2.4	42.66	58409	2939	99.98	0.2083	0.2056	0.2111	0.2625	0.2655	RANDOM	39.963

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]
-1.05	-0.52		-1.05		3.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.171
r_dihedral_angle_4_deg	16.927
r_dihedral_angle_3_deg	16.494
r_dihedral_angle_1_deg	7.279
r_angle_refined_deg	1.63
r_angle_other_deg	1.271
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10475
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	285

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing