2PFJ | pdb_00002pfj

Crystal Structure of T7 Endo I resolvase in complex with a Holliday Junction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FZR	Globular domain from pdb file 1FZR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	20 mM CaCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.977	α = 90
b = 92.977	β = 90
c = 124.265	γ = 120

Symmetry
Space Group	P 32 2 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	MARMOSAIC 225 mm CCD	Pt coated Si mirrors	2006-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	30	99.4	0.052	14.8	3.6	11646	11577	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.175	100		0.344	2.8	3.6	776

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	Globular domain from pdb file 1FZR	3.1	11.93	10851	538	99.37	0.26848	0.26704	0.26	0.29776	0.29	RANDOM	96.457

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]
-0.02	-0.01		-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.712
r_dihedral_angle_3_deg	19.532
r_dihedral_angle_4_deg	10.965
r_dihedral_angle_1_deg	5.743
r_scangle_it	2.598
r_angle_refined_deg	1.893
r_scbond_it	1.172
r_mcangle_it	1.085
r_mcbond_it	0.64
r_nbtor_refined	0.313
r_nbd_refined	0.229
r_metal_ion_refined	0.193
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.116
r_symmetry_hbond_refined	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2139
Nucleic Acid Atoms	1098
Solvent Atoms
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing