2GV9 | pdb_00002gv9

Crystal structure of the Herpes Simplex virus type 1 DNA polymerase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		100mM HEPES, 50mM ammonium sulphate, 5mM DTT, 100mM guanidine-HCl, 4% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.917	α = 90
b = 125.55	β = 90
c = 220.577	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	CCD	ADSC QUANTUM 315		2002-11-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0, 0.9794, 0.9504	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.675	48.3	100	0.071	30.2	9.1	81295	81295	4	2.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.675	2.8	100		0.849	2.4	8.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.68	48.3	77153	4070	98.88	0.2248	0.22182	0.22	0.28057	0.28	RANDOM	52.287

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]
-0.64			0.3		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.247
r_dihedral_angle_3_deg	20.681
r_dihedral_angle_4_deg	19.384
r_dihedral_angle_1_deg	7.824
r_scangle_it	2.51
r_angle_refined_deg	1.815
r_scbond_it	1.707
r_mcangle_it	1.137
r_angle_other_deg	1.016
r_mcbond_it	0.918
r_symmetry_vdw_other	0.317
r_nbd_refined	0.249
r_nbd_other	0.208
r_nbtor_refined	0.198
r_xyhbond_nbd_refined	0.18
r_symmetry_hbond_refined	0.167
r_symmetry_vdw_refined	0.154
r_mcbond_other	0.137
r_chiral_restr	0.099
r_nbtor_other	0.097
r_xyhbond_nbd_other	0.029
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15905
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
SHELXS	phasing