6TIB

Structure of A. niger Fdc I327S variant in complex with 2 naphthoic 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
2.37	48.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.642	α = 90
b = 63.592	β = 90
c = 87.741	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		2018-07-14	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)	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	1.07	87.74	95.6	0.158	1	6.5	6.5		169880

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	1.07	1.17	73.9		1.127	0.7	1.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	4ZAA	1.07	87.74	169880	8543	72.058	0.126	0.1243	0.1519	12.67

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]
0.363			-0.335		-0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.929
r_dihedral_angle_4_deg	22.231
r_dihedral_angle_3_deg	11.822
r_dihedral_angle_1_deg	6.774
r_rigid_bond_restr	5.293
r_scangle_it	4.531
r_scangle_other	4.53
r_scbond_other	4.072
r_scbond_it	4.071
r_lrange_it	3.888
r_lrange_other	3.443
r_angle_refined_deg	2.148
r_mcangle_other	2.122
r_mcangle_it	2.09
r_mcbond_it	2.046
r_mcbond_other	1.968
r_angle_other_deg	1.676
r_symmetry_nbd_refined	0.33
r_nbd_other	0.292
r_symmetry_xyhbond_nbd_refined	0.29
r_nbd_refined	0.265
r_xyhbond_nbd_refined	0.229
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.18
r_chiral_restr	0.142
r_metal_ion_refined	0.097
r_symmetry_nbtor_other	0.088
r_gen_planes_refined	0.023
r_bond_refined_d	0.02
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3850
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms	60

Software

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