4ZA4 | pdb_00004za4

Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Initial screening of 0.3 microl 14 mg/ml A. niger Fdc1 in 100 mM NaCl, 25 mM Tris pH 7.5 and 0.3 microl reservoir solution at 4C resulted in a number of hits including PACT condition F4 (molecular dimensions). Seed stock produced from these crystals was used in an optimization screen based around 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350 mixing 0.05 microl seed stock, 0.25 microl protein solution and 0.3 microl reservoir solution at 4C.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.99	α = 90
b = 63.93	β = 90
c = 87.63	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	PSI PILATUS 6M		2014-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.987	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.22	33.82	99.96	0.037	11.2	6.1		152260

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.22	1.25	99.99		0.354	2	5.8

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	1.22	33.82	152260	8041	99.96	0.14652	0.14573	0.15	0.16111	0.16	RANDOM	9.809

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]
1.04			-2.27		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.569
r_dihedral_angle_4_deg	21.066
r_dihedral_angle_3_deg	12.311
r_mcbond_other	7.517
r_dihedral_angle_1_deg	6.603
r_scangle_it	6.569
r_rigid_bond_restr	5.09
r_scbond_it	4.873
r_angle_other_deg	4.393
r_mcangle_it	3.096
r_angle_refined_deg	2.384
r_mcbond_it	2.338
r_chiral_restr	0.158
r_bond_refined_d	0.028
r_gen_planes_other	0.02
r_gen_planes_refined	0.018
r_bond_other_d
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3847
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms	39

Software

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