5M1F | pdb_00005m1f

Crystal structure of the large terminase nuclease from thermophilic phage G20c

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2 M Lithium Sulfate, 0.1 M Bis-tris pH 5.5, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.102	α = 90
b = 55.102	β = 90
c = 95.759	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	PIXEL	DECTRIS PILATUS 6M-F		2016-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.15	47.72	95.6	0.043	0.055	0.035	0.999	10.3	2.2		9183

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	90.6		0.804	1.043	0.658	0.365		2.2	721

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	SAD	THROUGHOUT	2.15	47.72	8735	433	94.96	0.2044	0.2004	0.21	0.2811	0.29	RANDOM	54.596

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]
0.27	0.14		0.27		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.342
r_dihedral_angle_3_deg	12.077
r_dihedral_angle_4_deg	11.384
r_dihedral_angle_1_deg	6.177
r_mcangle_it	4.68
r_mcbond_it	3.1
r_mcbond_other	3.1
r_angle_refined_deg	1.291
r_angle_other_deg	0.861
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1407
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing