3V1Z | pdb_00003v1z

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	PDB ENTRY 1KNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	293	100mM Na-acetate pH 4.25-5.5, 10mM CaCl2 or CaAc2, 4-8% (w/v) of PEG8000, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.008	α = 90
b = 83.632	β = 90
c = 123.336	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 225 mm CCD		2005-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12		EMBL/DESY, HAMBURG	X12

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	2.2	69.14	99.1	0.067	0.067	16.7	3.8		33372			39.35

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	2.3	2.42	95.2		0.307	0.307	2.5	3.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1KNV	2.2	62.14	38563	33238	3719	95.9	0.232	0.226	0.22	0.283	0.27	RANDOM	42.3

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]
-1.34			3.75		-2.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.749
r_dihedral_angle_4_deg	16.181
r_dihedral_angle_3_deg	14.788
r_dihedral_angle_1_deg	5.267
r_scangle_it	1.156
r_angle_refined_deg	1.009
r_scbond_it	0.721
r_mcangle_it	0.604
r_mcbond_it	0.329
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4695
Nucleic Acid Atoms	526
Solvent Atoms	218
Heterogen Atoms

Software

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