7QF2 | pdb_00007qf2

Structure of miniSOG reconstituted with riboflavin as a cofactor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GPU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM Tris-HCl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 15 mM CoCl2

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.9	α = 90
b = 39.9	β = 90
c = 134.1	γ = 90

Symmetry
Space Group	P 43 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	TOROIDAL MIRROR	2014-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.973	ESRF	ID23-1

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	38.25	100	0.09	0.99	11.5	6.5		91259			12.4

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	1.1	99.9		1.12	0.563	1.12	5.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6GPU	1.07	38.243	48984	2357	99.973	0.131	0.1302	0.13	0.1553	0.16	12.796

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]
-0.158			-0.158		0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.531
r_dihedral_angle_4_deg	19.6
r_dihedral_angle_3_deg	15.169
r_dihedral_angle_1_deg	6.81
r_rigid_bond_restr	5.852
r_lrange_it	3.648
r_lrange_other	3.423
r_scangle_it	3.369
r_scangle_other	3.367
r_scbond_it	2.842
r_scbond_other	2.84
r_mcbond_it	2.367
r_mcbond_other	2.334
r_mcangle_it	2.243
r_mcangle_other	2.241
r_angle_refined_deg	2.2
r_angle_other_deg	1.529
r_symmetry_xyhbond_nbd_refined	0.347
r_xyhbond_nbd_refined	0.341
r_nbd_refined	0.289
r_symmetry_nbd_refined	0.263
r_nbd_other	0.233
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.188
r_chiral_restr	0.138
r_symmetry_nbtor_other	0.094
r_metal_ion_refined	0.04
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	947
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	36

Software

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