9RJT | pdb_00009rjt

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Dithionite reduced - anaerobic soaked with 58 bar CO2 for 1 min

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.993	α = 90
b = 124.845	β = 90
c = 150.48	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 4M		2022-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	1.83	64.442	88.57	0.9887	8.518	8.53		73531

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	1.83	1.988			0.4894

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	FREE R-VALUE	1.83	64.442	73468	3726	67.649	0.193	0.1902	0.199	0.2405	0.2465	23.749

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]
0.072			0.002		-0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.498
r_dihedral_angle_4_deg	20.046
r_dihedral_angle_3_deg	13.832
r_dihedral_angle_1_deg	7.174
r_lrange_it	6.406
r_lrange_other	6.388
r_scangle_it	4.775
r_scangle_other	4.77
r_mcangle_other	3.879
r_mcangle_it	3.878
r_scbond_it	3.189
r_scbond_other	3.18
r_mcbond_it	2.66
r_mcbond_other	2.659
r_angle_refined_deg	1.374
r_angle_other_deg	1.188
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.195
r_symmetry_nbd_other	0.18
r_nbd_other	0.175
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.112
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.005
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	9213
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	227

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
XDS	data reduction
Aimless	data scaling
XSCALE	data scaling
pointless	data scaling