9PUA | pdb_00009pua

L-Biotin-streptavidin binding

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	294	1 micro-liter protein containing 3 mM Biotin in 10 mM Tris-HCl pH 7.0 mixed with 1 micro-liter 38% Ammonium Sulfate, 100 mM Na-Acetate pH 4.5, 200 mM NaCl at 21C (294 K)

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.688	α = 90
b = 94.415	β = 90
c = 105.14	γ = 90

Symmetry
Space Group	I 2 2 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		2022-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9600	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	0.94	41.886	93.7	0.009	1	31.4	35.1		139644

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.94	0.96	71.6		0.798	0.449	0.8	20.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	0.944	41.886	138990	2769	93.465	0.127	0.1262	0.133	0.1466	0.15	12.615

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]
-0.439			1.456		-1.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.118
r_dihedral_angle_4_deg	21.708
r_rigid_bond_restr	13.753
r_dihedral_angle_3_deg	11.297
r_dihedral_angle_1_deg	8.198
r_lrange_it	4.287
r_lrange_other	4.286
r_mcangle_other	3.862
r_mcangle_it	3.843
r_scangle_it	3.767
r_scangle_other	3.766
r_mcbond_it	3.389
r_mcbond_other	3.059
r_scbond_it	2.968
r_scbond_other	2.966
r_angle_refined_deg	2.473
r_angle_other_deg	1.121
r_chiral_restr	1.036
r_symmetry_nbd_refined	0.875
r_nbd_other	0.439
r_symmetry_xyhbond_nbd_refined	0.291
r_symmetry_nbd_other	0.218
r_nbd_refined	0.203
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.168
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.028
r_gen_planes_refined	0.015
r_symmetry_xyhbond_nbd_other	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1815
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing