6EV3 | pdb_00006ev3

Structure of wild type A. niger Fdc1 that has been illuminated with UV light, with prFMN in the iminium and ketimine form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZA4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.131	α = 90
b = 63.906	β = 90
c = 87.853	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		2016-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.3	64.85	96.4	7.4	3.7		475106

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	1.3	1.346			1.223	0.5	1.1	3.7

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 (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	4ZA4	1.3	64.85	121466	6290	95.85	0.17424	0.17307	0.17	0.19711	0.2	RANDOM	14.446

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]
-0.51			0.76		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.553
r_dihedral_angle_4_deg	20.76
r_dihedral_angle_3_deg	11.892
r_long_range_B_refined	11.122
r_long_range_B_other	11.045
r_dihedral_angle_1_deg	6.429
r_scangle_other	2.981
r_angle_refined_deg	2.244
r_scbond_other	2.077
r_scbond_it	2.076
r_mcangle_other	1.833
r_mcangle_it	1.83
r_mcbond_it	1.288
r_mcbond_other	1.288
r_angle_other_deg	1.181
r_chiral_restr	0.161
r_bond_refined_d	0.023
r_gen_planes_refined	0.015
r_gen_planes_other	0.005
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3852
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms	75

Software

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