3V21 | pdb_00003v21

Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	0.1 M Bis-Tris, 0.5% polyvinylpyrrolidone and 16% of PEG400, VAPOR DIFFUSION, temperature 293K, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.88	α = 90
b = 115.311	β = 112.5
c = 130.243	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MAR555		2007-10-01		SINGLE WAVELENGT

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8148	EMBL/DESY, HAMBURG	X11

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	2.326	65.094	100	0.061	0.061	20.3	4.6	80299	80299			66.976

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	2.7	2.85	100		0.388	0.388	1.9	4.6	11696

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	MR	THROUGHOUT	1knv	2.7	65.09	80279	80279	7973	99.98	0.23372	0.234	0.23	0.23	0.267	0.26	RANDOM	54.404

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]
-0.54		-0.54	-0.13		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.442
r_dihedral_angle_4_deg	21.622
r_dihedral_angle_3_deg	15.206
r_angle_other_deg	3.82
r_mcangle_it	2.099
r_scangle_it	1.878
r_dihedral_angle_1_deg	1.542
r_angle_refined_deg	1.288
r_mcbond_it	1.183
r_scbond_it	1.122
r_symmetry_vdw_other	0.312
r_nbd_other	0.273
r_nbd_refined	0.244
r_symmetry_vdw_refined	0.23
r_nbtor_refined	0.203
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.115
r_xyhbond_nbd_other	0.11
r_nbtor_other	0.107
r_chiral_restr	0.089
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18735
Nucleic Acid Atoms	3562
Solvent Atoms	359
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOLREP	phasing