8RCC | pdb_00008rcc

W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soaked with 48 bar CO2 for 1 min

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	8	293	22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.81	α = 90
b = 124.401	β = 90
c = 150.307	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 R 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	2.301	95.835	89.19	0.9854	6.55	5.6		45048

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	2.301	2.44			0.465

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	2.301	95.835	45013	2267	82.201	0.196	0.1938	0.2	0.2442	0.25	33.536

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]
0.131			-0.007		-0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.551
r_dihedral_angle_4_deg	18.145
r_dihedral_angle_3_deg	16.189
r_dihedral_angle_1_deg	7.349
r_lrange_it	5.377
r_lrange_other	5.377
r_scangle_it	3.571
r_scangle_other	3.571
r_mcangle_it	3.464
r_mcangle_other	3.464
r_scbond_it	2.295
r_scbond_other	2.292
r_mcbond_it	2.239
r_mcbond_other	2.237
r_angle_refined_deg	1.36
r_angle_other_deg	1.145
r_symmetry_nbd_refined	0.264
r_nbd_other	0.215
r_nbd_refined	0.198
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.057
r_symmetry_xyhbond_nbd_refined	0.051
r_symmetry_xyhbond_nbd_other	0.008
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	9199
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	242

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