7QF4 | pdb_00007qf4

Structure of the R57Q mutant of miniSOG expressed in E. coli in LB medium enriched with riboflavin

X-RAY DIFFRACTION

---

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
2.06	40.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.93	α = 90
b = 39.93	β = 90
c = 134.65	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 PILATUS3 6M	TOROIDAL MIRROR	2015-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.984	ESRF	ID29

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	1.17	38.29	99.7	0.06	0.999	17.9	8.1		37774			15.8

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	1.17	1.2	99.1		1	0.646	2

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	1.17	38.282	37774	1800	99.633	0.148	0.1464	0.15	0.1821	0.18	13.87

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]
-0.224			-0.224		0.448

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.341
r_dihedral_angle_4_deg	19.366
r_dihedral_angle_3_deg	13.094
r_dihedral_angle_1_deg	6.949
r_rigid_bond_restr	4.287
r_lrange_it	3.167
r_scangle_it	3.067
r_scangle_other	3.065
r_lrange_other	3.008
r_scbond_it	2.665
r_scbond_other	2.663
r_angle_refined_deg	2.167
r_mcangle_other	1.695
r_mcangle_it	1.628
r_angle_other_deg	1.53
r_mcbond_it	1.435
r_mcbond_other	1.291
r_nbd_refined	0.252
r_nbd_other	0.23
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.123
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	942
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	29

Software

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