7YL4 | pdb_00007yl4

Cell surface protein YwfG protein (apo form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M01

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium acetate (pH 5.0-5.6), 1.3 M Li2SO4, 2% (w/v) polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
4.37	71.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.219	α = 90
b = 272.93	β = 90
c = 320.332	γ = 90

Symmetry
Space Group	I 2 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	95	PIXEL	DECTRIS PILATUS3 S 6M		2018-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.5	48.6	100	0.092	0.096	0.026	0.999	21.3	13		66894

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	100		0.809	0.841	0.229	0.871	3.4	13.3

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	4m01	2.5	45.53	66893	3224	99.969	0.247	0.2455	0.25	0.2796	0.28	65.081

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]
-5.041			4.543		0.499

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.665
r_dihedral_angle_3_deg	21.114
r_dihedral_angle_4_deg	17.235
r_lrange_it	13.365
r_lrange_other	13.359
r_scangle_it	10.846
r_scangle_other	10.719
r_mcangle_it	10.373
r_mcangle_other	10.373
r_scbond_it	7.47
r_scbond_other	7.352
r_mcbond_other	7.323
r_mcbond_it	7.322
r_dihedral_angle_1_deg	7.095
r_angle_refined_deg	1.754
r_angle_other_deg	1.345
r_metal_ion_refined	0.274
r_nbd_other	0.231
r_nbd_refined	0.202
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.171
r_symmetry_nbd_refined	0.162
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.065
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6527
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing