4XLH | pdb_00004xlh

Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1 M Tris-HCl, 3.5 M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.975	α = 90
b = 73.975	β = 90
c = 174.328	γ = 120

Symmetry
Space Group	P 3 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	RAYONIX MX-225	mirrors	2012-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.91	43.04	99.6	0.107	0.051	0.998	14.1	5.4		43960

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.95	94		0.761	0.368	0.652	2.1	5.1	2752

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	4XM3	1.91	43.04	43960	2189	99.93	0.1601	0.1574	0.1678	0.2104	0.2198	RANDOM	23.005

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]
0.52	0.26		0.52		-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.441
r_dihedral_angle_4_deg	15.834
r_dihedral_angle_3_deg	12.259
r_dihedral_angle_1_deg	7.235
r_angle_refined_deg	1.674
r_mcangle_it	1.285
r_mcbond_other	0.876
r_mcbond_it	0.87
r_angle_other_deg	0.853
r_chiral_restr	0.104
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4540
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	24

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
ARP	model building
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing