7QF5 | pdb_00007qf5

Structure of the Q103L mutant of miniSOG

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
2.06	40.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.05	α = 90
b = 40.05	β = 90
c = 134.26	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	2015-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9789	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	1.37	38.38	99.9	0.06	1	23.9	8.3		23979			21.4

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	1.37	1.41			1.07	0.643	2.1

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	1.37	38.379	23979	1152	99.937	0.128	0.1257	0.13	0.1739	0.18	17.635

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]
0.076			0.076		-0.152

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.885
r_dihedral_angle_4_deg	19.202
r_dihedral_angle_3_deg	12.602
r_dihedral_angle_1_deg	6.562
r_lrange_it	3.634
r_lrange_other	3.366
r_scangle_it	2.665
r_scangle_other	2.663
r_scbond_other	2.17
r_scbond_it	2.164
r_mcangle_other	2.008
r_mcangle_it	1.997
r_rigid_bond_restr	1.817
r_angle_refined_deg	1.62
r_mcbond_it	1.587
r_mcbond_other	1.475
r_angle_other_deg	1.382
r_symmetry_xyhbond_nbd_refined	0.254
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.219
r_symmetry_nbd_refined	0.217
r_nbd_other	0.188
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.178
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_metal_ion_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	938
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	34

Software

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