2Y32 | pdb_00002y32

Crystal structure of bradavidin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AVD	AN ENSEMBLE OF THREE HOMOLOGY MODELS OF BRADAVIDIN BASED ON PDB ENTRIES 1AVD, 1MK5, AND 2UYW.
experimental model	PDB	1MK5	AN ENSEMBLE OF THREE HOMOLOGY MODELS OF BRADAVIDIN BASED ON PDB ENTRIES 1AVD, 1MK5, AND 2UYW.
experimental model	PDB	2UYW	AN ENSEMBLE OF THREE HOMOLOGY MODELS OF BRADAVIDIN BASED ON PDB ENTRIES 1AVD, 1MK5, AND 2UYW.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			0.7 MICROLITER OF WELL SOLUTION CONTAINING 25% PEG 4000, 0.17 M AMMONIUM ACETATE, AND 0.08 M SODIUM ACETATE, PH 4.6 WERE MIXED WITH 0.8 MICROLITER OF PROTEIN SOLUTION CONTAINING 0.4 MG PER ML OF PROTEIN, 50 MM SODIUM ACETATE, PH 4. THE PROTEIN SOLUTION WAS DILUTED WITH SATURATED SOLUTION OF 4-HYDROXYAZOBENZENE-2-CARBOXYLIC ACID IN 1 TO 10 VOLUME RATIO BEFORE CRYSTALLIZATION, WHICH WAS AT RT USING THE VAPOUR DIFFUSION METHOD AND SITTING DROPS.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.712	α = 90
b = 84.868	β = 90
c = 120.26	γ = 90

Symmetry
Space Group	P 21 21 21

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 SX-165		2006-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	1.78	25	100	0.09	18	9.6		46670		-3

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	1.78	1.88	100		0.42	5.9	9.6

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	AN ENSEMBLE OF THREE HOMOLOGY MODELS OF BRADAVIDIN BASED ON PDB ENTRIES 1AVD, 1MK5, AND 2UYW.	1.78	28.64	44303	2365	100	0.14639	0.1444	0.14	0.18243	0.18	RANDOM	18.011

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]
-0.35			0.18		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.523
r_dihedral_angle_3_deg	11.221
r_dihedral_angle_1_deg	5.904
r_scangle_it	3.159
r_scbond_it	2.142
r_angle_refined_deg	1.382
r_mcangle_it	1.346
r_mcbond_it	0.76
r_chiral_restr	0.112
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	4034
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms

Software

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