8S7S | pdb_00008s7s

Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151G mutant

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	EVAPORATION		293	G4 condition of the morpheus crystal screen by Hampton Research

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.804	α = 90
b = 144.145	β = 90
c = 289.452	γ = 90

Symmetry
Space Group	C 2 2 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 2M		2023-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.967700	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.5	64.6	100	0.202	0.207	0.043	0.997	12.5	22.8		66056

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56		100	3.274	3.346	0.686	0.605		23.6

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 (Observed)	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	2.5	64.6	62822	3182	99.98	0.19494	0.192	0.1992	0.25173	0.254	RANDOM	56.371

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]
2.8			-0.13		-2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.184
r_long_range_B_other	10.367
r_long_range_B_refined	10.365
r_scangle_other	8.366
r_dihedral_angle_2_deg	8.265
r_dihedral_angle_1_deg	7.82
r_mcangle_it	7.339
r_mcangle_other	7.339
r_scbond_it	5.725
r_scbond_other	5.725
r_mcbond_it	5.161
r_mcbond_other	5.161
r_angle_refined_deg	1.515
r_angle_other_deg	0.506
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12234
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	159

Software

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