Experiment: 8XBR

Crystal structure of activity improved formolase variant K3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M2Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M Na/K phosphate pH 6.2, 0.2 M NaCl , 36% (v/v) PEG-400

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.165	α = 90
b = 99.19	β = 90
c = 110.544	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		2022-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17UM	0.987	SSRF	BL17UM

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	1.92	50	99.7	0.151	0.158	0.043	0.99	3.7	13		41453

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	1.92	1.99	97.4		0.913	0.97	0.318	0.75		8.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.92	49.08	1.35	41345	2055	99.2	0.1505	0.149	0.1603	0.1778	0.1837

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.377
f_angle_d	1.455
f_chiral_restr	0.093
f_plane_restr	0.022
f_bond_d	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3936
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	27

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing