6TIJ | pdb_00006tij

Structure of A. niger Fdc WT in complex with indol-2-carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.781	α = 90
b = 63.725	β = 90
c = 87.707	γ = 90

Symmetry
Space Group	P 21 21 2

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-F		2018-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.975	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.12	64.79	99.5	0.093	1	9.3	6		204931

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.12	1.14	91.9		0.739	0.5	1.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	4ZAA	1.12	64.685	202805	10012	98.513	0.141	0.1397	0.14	0.1686	0.17	12.659

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]
-0.022			-0.149		0.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.405
r_dihedral_angle_4_deg	21.99
r_dihedral_angle_3_deg	11.803
r_dihedral_angle_1_deg	6.783
r_rigid_bond_restr	5.227
r_lrange_it	4.183
r_lrange_other	4.183
r_scangle_other	3.633
r_scangle_it	3.632
r_scbond_it	3.117
r_scbond_other	3.117
r_angle_refined_deg	2.224
r_mcangle_other	2.194
r_mcangle_it	2.191
r_mcbond_it	2.014
r_mcbond_other	2.004
r_angle_other_deg	1.686
r_symmetry_xyhbond_nbd_refined	0.302
r_nbd_refined	0.254
r_xyhbond_nbd_other	0.231
r_nbd_other	0.225
r_xyhbond_nbd_refined	0.22
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.181
r_chiral_restr	0.149
r_metal_ion_refined	0.092
r_symmetry_nbtor_other	0.09
r_gen_planes_refined	0.024
r_bond_refined_d	0.02
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3852
Nucleic Acid Atoms
Solvent Atoms	656
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling