4Z28

Crystal structure of short hoefavidin biotin complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Streak seeding was applied with source crystals. Crystals appeared within 24 hours and grew to their maximal size within 2 weeks

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.18	α = 90
b = 61.18	β = 90
c = 166.86	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97	ESRF	ID29

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	1.66	50	99.8	0.045	19.9	6.9		38372

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	1.66	1.72			0.798

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4Z27	1.66	50	36448	1924	99.81	0.18194	0.17955	0.23017	RANDOM	33.531

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]
-2.02			-2.02		4.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.702
r_dihedral_angle_2_deg	39.761
r_sphericity_bonded	26.693
r_dihedral_angle_3_deg	13.643
r_scangle_other	8.931
r_scbond_it	7.619
r_scbond_other	7.619
r_long_range_B_other	7.11
r_long_range_B_refined	7.105
r_dihedral_angle_1_deg	6.996
r_mcangle_other	6.451
r_mcangle_it	6.448
r_mcbond_it	5.337
r_mcbond_other	5.331
r_rigid_bond_restr	4.344
r_angle_refined_deg	1.791
r_angle_other_deg	1.486
r_chiral_restr	0.113
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_4_deg
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1907
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
MOLREP	phasing
XSCALE	data scaling