Experiment: 7AE5

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M1C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	Molecular Dimensions BCS H2: 0.1 M Hepes, pH 7.5, 30% v/v PEG Smear low

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.23	α = 117.72
b = 108.3	β = 101.32
c = 111.42	γ = 91.8

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS PILATUS3 6M		2018-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.19	70.15	97.03	0.05937	0.08396	0.984	6.59	1.8		197121			43.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.268	95.74		0.563	0.7962	0.445	1.42	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5M1C	2.19	70.14	1.96	197044	9805	97.03	0.2253	0.2233	0.223	0.2625	0.2616	56.9

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.7921
f_angle_d	0.6162
f_chiral_restr	0.0479
f_plane_restr	0.0054
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24495
Nucleic Acid Atoms
Solvent Atoms	804
Heterogen Atoms	18

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing