6F73 | pdb_00006f73

Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IPI	2IPI, 2BVF, 2Y08, 3W8W,3RJ8
experimental model	PDB	2BVF	2IPI, 2BVF, 2Y08, 3W8W,3RJ8
experimental model	PDB	2Y08	2IPI, 2BVF, 2Y08, 3W8W,3RJ8
experimental model	PDB	3W8W	2IPI, 2BVF, 2Y08, 3W8W,3RJ8
experimental model	PDB	3RJ8	2IPI, 2BVF, 2Y08, 3W8W,3RJ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	294	20% PEG6000, , 0.2 M NaCl, 0.1 M NaAcetate pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.9	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.417	α = 90
b = 115.959	β = 90
c = 198.676	γ = 90

Symmetry
Space Group	P 2 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	110	IMAGE PLATE	MARRESEARCH		2015-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.22	58	99.5	0.147	0.081	0.995	12.9	8		71982			13.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.27	92.8		0.514	0.225	0.706	3.7	6.7

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	2IPI, 2BVF, 2Y08, 3W8W,3RJ8	2.22	58	68291	3610	99.48	0.19489	0.1928	0.2	0.23467	0.24	RANDOM	36.81

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]
0.03			0.46		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.009
r_dihedral_angle_4_deg	16.002
r_dihedral_angle_3_deg	12.926
r_long_range_B_other	9.446
r_long_range_B_refined	9.431
r_scangle_other	7.105
r_scbond_it	5.97
r_dihedral_angle_1_deg	5.969
r_scbond_other	5.969
r_angle_other_deg	3.844
r_mcangle_it	3.162
r_mcangle_other	3.161
r_mcbond_it	2.41
r_mcbond_other	2.41
r_angle_refined_deg	1.333
r_chiral_restr	0.073
r_gen_planes_other	0.029
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8364
Nucleic Acid Atoms
Solvent Atoms	847
Heterogen Atoms	260

Software

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