2VNL | pdb_00002vnl

MUTANT Y108Wdel OF THE HEADBINDING DOMAIN OF PHAGE P22 TAILSPIKE C- TERMINally fused to ISOLEUCINE ZIPPER pIIGCN4 (chimera II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LKT	PDB ENTRIES 1LKT, 1EBO
experimental model	PDB	1EBO	PDB ENTRIES 1LKT, 1EBO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		VAPOR DIFFUSION, HANGING DROP. PROTEIN: CONC. 9.3 MG/ML,BUFFER 50MM HEPES, PH6.5; RESERVOIR:20% ISOPROPANOL, 0.1M NA-ACETATE, PH4.6, 0.2M CACL2; DROPLET 2 MICROL:2 MICROL.CRYO:30% GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.012	α = 90
b = 58.012	β = 90
c = 156.11	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	CCD	MARRESEARCH	MIRRORS	2006-10-27	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	1.8	50	98.5	0.05	22.5	7.3		17904

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	1.8	1.93	95.5		0.38	5	7.3

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 ENTRIES 1LKT, 1EBO	1.8	19.37	17174	934	99.7	0.192	0.19	0.2	0.229	0.23	RANDOM	31.35

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.041
r_dihedral_angle_3_deg	12.989
r_dihedral_angle_4_deg	7.497
r_dihedral_angle_1_deg	5.715
r_scangle_it	2.597
r_mcangle_it	1.99
r_scbond_it	1.929
r_mcbond_it	1.722
r_angle_refined_deg	1.287
r_angle_other_deg	0.854
r_symmetry_vdw_other	0.242
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.192
r_nbd_other	0.174
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.149
r_nbtor_other	0.085
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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	1158
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	18

Software

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