6TJZ | pdb_00006tjz

Crystal structure of the SVS_A2 protein (W156Y mutant) from ancestral sequence reconstruction at 2.4 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.3 18% PEG 3350 Cryoprotection: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.3 24% PEG 3350 5mM MgCl2 5 mM FPP

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.882	α = 90
b = 104.583	β = 90
c = 109.24	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	PIXEL	DECTRIS EIGER X 16M	KB mirrors	2019-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.91841	MAX IV	BioMAX

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	2.4	40.66	100	0.064	0.031	0.999	10.8	5.6		34301			61.5

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	2.4	2.49	99.9		0.642	0.353	0.739	1.9	5

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	4OKZ	2.4	25	32300	1735	99.35	0.1821	0.1799	0.19	0.2208	0.22	RANDOM	63.92

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]
0.01			-1.82		1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.944
r_dihedral_angle_4_deg	19.419
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_1_deg	6.243
r_angle_refined_deg	1.533
r_angle_other_deg	1.318
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.944
r_dihedral_angle_4_deg	19.419
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_1_deg	6.243
r_angle_refined_deg	1.533
r_angle_other_deg	1.318
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_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	5206
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

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

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.