7QF3 | pdb_00007qf3

Structure of the R57Q mutant of miniSOG expressed in E. coli in regular LB medium

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	39.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.951	α = 90
b = 39.951	β = 90
c = 133.581	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	2014-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9322	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	1.1	38.28	100	0.084	1	15.5	12.4		45101			14.5

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	1.1	1.14	100		1.199	0.596	1.9	11.9

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	1.1	38.28	45100	2275	99.971	0.145	0.1443	0.15	0.1702	0.17	13.784

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]
-0.201			-0.201		0.401

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.412
r_dihedral_angle_4_deg	16.212
r_dihedral_angle_3_deg	13.574
r_dihedral_angle_1_deg	7.136
r_scangle_it	4.193
r_scangle_other	4.191
r_rigid_bond_restr	4.052
r_scbond_other	3.847
r_scbond_it	3.839
r_lrange_it	3.598
r_lrange_other	3.531
r_angle_refined_deg	2.246
r_mcangle_other	2.045
r_mcangle_it	2.009
r_mcbond_it	1.636
r_mcbond_other	1.576
r_angle_other_deg	1.541
r_metal_ion_refined	0.328
r_symmetry_xyhbond_nbd_other	0.31
r_symmetry_xyhbond_nbd_refined	0.297
r_symmetry_nbd_refined	0.293
r_nbd_other	0.274
r_nbd_refined	0.232
r_symmetry_nbd_other	0.207
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.195
r_chiral_restr	0.132
r_symmetry_nbtor_other	0.093
r_bond_refined_d	0.02
r_gen_planes_refined	0.015
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	941
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	34

Software

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