2VFP | pdb_00002vfp

Low Temperature Structure of P22 Tailspike Protein Fragment (109-666), Mutant V349L

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		10		DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.29	α = 90
b = 120.29	β = 90
c = 120.29	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARRESEARCH	MIRRORS	2006-10-29	M	SINGLE WAVELENGTH

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

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	1.59	50	93.3	0.06	26.1	10.5		72574			16.7

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	1.59	1.7	55.8		0.21	4	1.7

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 2VFO	1.55	49.09	70438	3699	87.6	0.125	0.123	0.14	0.152	0.16	RANDOM	9.37

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.203
r_dihedral_angle_4_deg	13.019
r_dihedral_angle_3_deg	11.808
r_dihedral_angle_1_deg	6.625
r_scangle_it	4.746
r_scbond_it	3.474
r_mcangle_it	2.236
r_mcbond_it	1.704
r_angle_refined_deg	1.376
r_angle_other_deg	0.792
r_symmetry_vdw_other	0.206
r_nbd_refined	0.2
r_nbd_other	0.185
r_symmetry_vdw_refined	0.176
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.085
r_nbtor_other	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	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	4215
Nucleic Acid Atoms
Solvent Atoms	776
Heterogen Atoms	42

Software

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