8QGR | pdb_00008qgr

Stopper protein of phage 812 in closed conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293.15	1.6 M NaCl, 8% PEG 6000, 20% glycerol, 3% dextran sulphate sodium

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.366	α = 90
b = 93.366	β = 90
c = 122.531	γ = 120

Symmetry
Space Group	P 6 2 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		2017-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97857	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	37.2	99.9	0.13	23.26	11.7		16664

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	99.8		0.689	4.21

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.2	37.159	16649	1632	99.844	0.193	0.19	0.1982	0.2192	0.227	31.435

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]
-1.375	-0.687		-1.375		4.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.971
r_dihedral_angle_3_deg	11.68
r_lrange_it	6.621
r_lrange_other	6.546
r_dihedral_angle_1_deg	5.954
r_scangle_it	4.721
r_scangle_other	4.719
r_mcangle_it	3.431
r_mcangle_other	3.43
r_dihedral_angle_2_deg	3.017
r_scbond_it	2.798
r_scbond_other	2.796
r_mcbond_it	2.129
r_mcbond_other	2.128
r_dihedral_angle_other_3_deg	2.014
r_angle_refined_deg	1.223
r_angle_other_deg	0.393
r_symmetry_nbd_other	0.217
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.199
r_nbtor_refined	0.179
r_nbd_other	0.178
r_symmetry_nbd_refined	0.168
r_symmetry_xyhbond_nbd_other	0.153
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.056
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1815
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	1

Software

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