9IHB | pdb_00009ihb

Crystal structure of vanillin dehydrogenase with covalently bound vanillin and cofactor NADH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	18 % w/v PEG 5000 MME, 0.2 M Ammonium sulfate, 0.1 M MES 6.5, 3 mM vanillin, 10 mM NAD+

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.069	α = 90
b = 150.837	β = 93.877
c = 150.404	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER2 XE 16M		2023-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.41	150.06	91	0.322	0.129	0.982	5.5	7.2		107071

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.41	2.588	67.3		1.373	0.543	0.553	1.6	7.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.41	150.06	107069	5571	67.847	0.197	0.1956	0.1955	0.2264	0.2264	RANDOM	32.469

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]
-0.798		-0.667	0.509		0.376

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.784
r_dihedral_angle_3_deg	14.681
r_dihedral_angle_2_deg	8.319
r_dihedral_angle_1_deg	6.398
r_lrange_it	5.925
r_scangle_it	4.478
r_scbond_it	2.905
r_mcangle_it	2.806
r_angle_refined_deg	1.935
r_mcbond_it	1.716
r_symmetry_xyhbond_nbd_refined	0.31
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.286
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.117
r_ncsr_local_group_19	0.046
r_ncsr_local_group_3	0.045
r_ncsr_local_group_14	0.045
r_ncsr_local_group_21	0.044
r_ncsr_local_group_2	0.043
r_ncsr_local_group_20	0.043
r_ncsr_local_group_1	0.041
r_ncsr_local_group_9	0.041
r_ncsr_local_group_16	0.041
r_ncsr_local_group_8	0.039
r_ncsr_local_group_22	0.039
r_ncsr_local_group_7	0.038
r_ncsr_local_group_17	0.038
r_ncsr_local_group_15	0.037
r_ncsr_local_group_18	0.037
r_ncsr_local_group_4	0.036
r_ncsr_local_group_6	0.036
r_ncsr_local_group_5	0.035
r_ncsr_local_group_12	0.034
r_ncsr_local_group_10	0.033
r_ncsr_local_group_11	0.032
r_ncsr_local_group_26	0.032
r_ncsr_local_group_23	0.031
r_ncsr_local_group_28	0.028
r_ncsr_local_group_25	0.027
r_ncsr_local_group_13	0.025
r_ncsr_local_group_27	0.024
r_ncsr_local_group_24	0.016
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27366
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	480

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing