2VBK | pdb_00002vbk

NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION HANGING DROP,20 DEGR. CELSIUS; DROP: 1 MICROL RESERVOIR AND 1 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.0,18% PEG8000, 20MM MNCL2; PROTEIN: 10MG/ML, 10MM NA-PHOSPHATE,PH7.0, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.231	α = 90
b = 96.231	β = 90
c = 182.433	γ = 120

Symmetry
Space Group	H 3

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		2000-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	1.25	20	97.4	0.05	11.6	2.2		169746			9.19

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	1.25	1.27	79.8		0.25	2	1.9

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 2VBE	1.25	14.92	161221	8511	97.4	0.12	0.119	0.13	0.142	0.15	RANDOM	10.2

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.687
r_scangle_it	5.346
r_scbond_it	4.256
r_mcangle_it	3.415
r_mcbond_it	2.879
r_angle_other_deg	2.389
r_angle_refined_deg	1.664
r_symmetry_vdw_other	0.322
r_nbd_other	0.277
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.103
r_nbtor_other	0.091
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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	3833
Nucleic Acid Atoms
Solvent Atoms	664
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing