5F2B | pdb_00005f2b

Expanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QCB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	1.5 M ammonium sulfate, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.465	α = 90
b = 57.465	β = 90
c = 173.564	γ = 90

Symmetry
Space Group	I 41 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 EIGER X 16M		2015-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	54.553	100	0.103	0.03	0.998	12.6	12.6		16547

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	100		2.018	0.577	0.509	1.3	13	837

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	2QCB	1.7	54.55	15764	760	99.97	0.1465	0.1437	0.16	0.2058	0.22	RANDOM	37.888

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]
-2.32			-2.32		4.64

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	65.16
r_dihedral_angle_2_deg	26.327
r_sphericity_bonded	25.539
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_4_deg	12.942
r_mcangle_it	8.362
r_dihedral_angle_1_deg	7.458
r_mcbond_it	7.06
r_mcbond_other	6.963
r_rigid_bond_restr	6.452

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	65.16
r_dihedral_angle_2_deg	26.327
r_sphericity_bonded	25.539
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_4_deg	12.942
r_mcangle_it	8.362
r_dihedral_angle_1_deg	7.458
r_mcbond_it	7.06
r_mcbond_other	6.963
r_rigid_bond_restr	6.452
r_angle_refined_deg	2.62
r_angle_other_deg	1.322
r_chiral_restr	0.171
r_bond_refined_d	0.032
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	915
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	53

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.