9QM0 | pdb_00009qm0

W-formate dehydrogenase U192C from Desulfovibrio vulgaris

X-RAY DIFFRACTION

---

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	34% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.396	α = 90
b = 123.099	β = 90
c = 147.189	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		2021-06-18	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	1.833	63.167	92.92	0.9884	5.959	4.83		74505

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	1.833	2.006			0.668

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	1.833	63.167	74504	3891	74.387	0.175	0.1723	0.1825	0.2135	0.2173	25.248

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]
0.215			-0.08		-0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.108
r_dihedral_angle_4_deg	18.579
r_dihedral_angle_3_deg	13.677
r_dihedral_angle_1_deg	6.888
r_lrange_it	6.771
r_lrange_other	6.762
r_scangle_other	5.793
r_scangle_it	5.776
r_scbond_other	4.197
r_mcangle_it	4.194
r_mcangle_other	4.194
r_scbond_it	4.18
r_mcbond_it	3.225
r_mcbond_other	3.222
r_angle_refined_deg	1.262
r_angle_other_deg	1.146
r_symmetry_xyhbond_nbd_refined	0.208
r_nbd_refined	0.186
r_nbd_other	0.176
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.158
r_symmetry_nbd_refined	0.14
r_symmetry_xyhbond_nbd_other	0.128
r_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.056
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9256
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	245

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