8CRP | pdb_00008crp

Streptavidin WT Co-TAML artificial metalloenzyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PK2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	2 M ammonium sulfate, 0.1 M sodium acetate pH 4.0 for soaking pH adjustment to pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.499	α = 90
b = 57.701	β = 107.442
c = 57.701	γ = 90

Symmetry
Space Group	C 1 2 1

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 EIGER X 16M		2022-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99988	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2	45.954	98.2	0.097	0.115	0.06	0.998	10.3	6.9		40202

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			1.377	1.624	0.852	0.577		7

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	THROUGHOUT	2	45.954	40182	1957	97.835	0.202	0.2018	0.21	0.214	0.22	40.897

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]
0.86		0.445	-0.756		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.227
r_dihedral_angle_3_deg	12.949
r_lrange_it	10.144
r_lrange_other	9.915
r_dihedral_angle_2_deg	9.811
r_dihedral_angle_1_deg	7.539
r_scangle_it	7.165
r_scangle_other	6.876
r_scbond_it	4.8
r_mcangle_it	4.661
r_mcangle_other	4.66
r_scbond_other	4.604
r_mcbond_it	3.337
r_mcbond_other	3.336
r_angle_refined_deg	1.741
r_angle_other_deg	0.495
r_nbd_refined	0.245
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.2
r_xyhbond_nbd_refined	0.126
r_symmetry_nbd_refined	0.118
r_symmetry_nbtor_other	0.088
r_nbd_other	0.086
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3696
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	191

Software

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