8CM4

W-formate dehydrogenase C872A from Desulfovibrio vulgaris - exposed to oxygen

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	22% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.299	α = 90
b = 126.897	β = 90
c = 260.94	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 PILATUS 6M		2020-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979181	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.3	148.12	99.5	0.99	8.4	4.5		108727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.37			0.698

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6sdr	2.3	48.312	108727	5427	99.779	0.203	0.2004	0.2	0.2561	0.26	42.628

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]
-2.308			3.506		-1.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.174
r_dihedral_angle_4_deg	18.154
r_dihedral_angle_3_deg	15.125
r_dihedral_angle_1_deg	7.309
r_lrange_it	5.701
r_lrange_other	5.698
r_scangle_it	4.001
r_scangle_other	4.001
r_mcangle_it	3.677
r_mcangle_other	3.677
r_scbond_it	2.446
r_scbond_other	2.446
r_mcbond_it	2.369
r_mcbond_other	2.367
r_angle_refined_deg	1.399
r_angle_other_deg	1.152
r_nbd_refined	0.192
r_nbd_other	0.181
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_xyhbond_nbd_other	0.079
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.072
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18540
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	291

Software

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