2V0S | pdb_00002v0s

crystal structure of a hairpin exchange variant (LR1) of the targeting LINE-1 retrotransposon endonuclease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VYB	PDB ENTRY 1VYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.25	44.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.698	α = 90
b = 67.648	β = 90
c = 128.278	γ = 90

Symmetry
Space Group	C 2 2 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 CCD	MIRRORS	2000-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.8	80	96.4	0.08	11.9	3		23062		2

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	1.8	1.89	98.6		0.442	2.7

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	PDB ENTRY 1VYB	1.8	80	21871	1190	95.6	0.19	0.188	0.21	0.226	0.24	RANDOM	15.97

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]
0.06			0.79		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.4
r_dihedral_angle_3_deg	12.078
r_dihedral_angle_4_deg	11.503
r_dihedral_angle_1_deg	5.843
r_scangle_it	3.686
r_scbond_it	2.711
r_mcangle_it	1.488
r_angle_refined_deg	1.398
r_mcbond_it	1.35
r_angle_other_deg	1.013
r_symmetry_hbond_refined	0.377
r_xyhbond_nbd_refined	0.23
r_symmetry_vdw_other	0.222
r_nbd_refined	0.213
r_nbd_other	0.2
r_chiral_restr	0.186
r_nbtor_refined	0.164
r_nbtor_other	0.085
r_symmetry_vdw_refined	0.061
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1827
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing