7ORX

Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QSI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	300	0.16 M ammonium sulfate, 20% PEG8000, 0.1 mM Mes pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.57	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.5	α = 90
b = 132.24	β = 90
c = 138.7	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 PILATUS 6M		2017-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97948	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	123.5	100	0.154	0.997	11.5	10		70459		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	100		2.187	0.461		10.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6QSI	2.6	90.423	70459	2975	99.99	0.196	0.1963	0.1946	0.2329	81.639

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]
5.019			-3.673		-1.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.876
r_dihedral_angle_3_deg	18.527
r_dihedral_angle_4_deg	18.073
r_lrange_other	8.051
r_lrange_it	8.05
r_dihedral_angle_1_deg	7.853
r_scangle_it	4.288
r_scangle_other	4.288
r_mcangle_it	4.016
r_mcangle_other	4.016
r_scbond_it	2.702
r_scbond_other	2.678
r_mcbond_it	2.432
r_mcbond_other	2.432
r_angle_refined_deg	1.803
r_angle_other_deg	1.339
r_metal_ion_refined	0.298
r_nbd_other	0.254
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.218
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.075
r_ncsr_local_group_1	0.042
r_ncsr_local_group_4	0.041
r_ncsr_local_group_5	0.038
r_ncsr_local_group_2	0.037
r_ncsr_local_group_6	0.037
r_ncsr_local_group_3	0.035
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15556
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	108

Software

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