2VJJ | pdb_00002vjj

TAILSPIKE PROTEIN OF E.COLI BACTERIOPHAGE HK620 IN COMPLEX WITH HEXASACCHARIDE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VJI	PDB ENTRY 2VJI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	VAPOR DIFFUSION, HANGING DROP: PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH8.0, 2 MM EDTA,0.2M NACL.RERVOIR: 20% ISOPROPANOL,0.1 M NA-ACETATE,PH6.0,0.2M CACL2. DROPLET 1.5:1.5 MICRO LITER. 30MM HEXASACCHARIDE. CRYO:30% GLYCEROL.TEMPERATURE 20 DEGREE CELSIUS.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.91	α = 90
b = 73.91	β = 90
c = 174.59	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	IMAGE PLATE	MARRESEARCH	MIRRORS	2006-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.58	19.2	95.6	0.04	26.7	83.5		73235			10.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.64	83.5		0.13	10.9	4.1

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	PDB ENTRY 2VJI	1.59	43.64	69829	3711	96.9	0.134	0.133	0.14	0.165	0.17	RANDOM	8.74

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]
0.23	0.12		0.23		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.356
r_dihedral_angle_4_deg	15.07
r_dihedral_angle_3_deg	11.337
r_scangle_it	7.812
r_dihedral_angle_1_deg	7.069
r_scbond_it	5.217
r_mcangle_it	3.162
r_mcbond_it	2.292
r_angle_other_deg	1.772
r_angle_refined_deg	1.303
r_symmetry_vdw_other	0.264
r_nbd_refined	0.252
r_nbd_other	0.221
r_symmetry_vdw_refined	0.196
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.136
r_nbtor_other	0.102
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4536
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing