8S4S | pdb_00008s4s

PrgE from plasmid pCF10

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, SITTING DROP		293	0.2 M LiSO4, 0.1 M K Phos Cit pH 4.2, 20 %w/v PEG 1K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.175	α = 90
b = 58.17	β = 90
c = 87.099	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 4M		2022-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	2.515	48.38	99.6	0.139	0.999	21.4	33.1		10486

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	2.515	2.56	100		1.718	0.852	2.39	35.04

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	48.377	8515	846	99.579	0.239	0.2345	0.24	0.2777	0.28	RANDOM	61.93

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]
-4.315			1.629		2.686

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.401
r_dihedral_angle_6_deg	11.708
r_dihedral_angle_1_deg	6.51
r_lrange_it	6.284
r_lrange_other	6.002
r_dihedral_angle_2_deg	4.2
r_mcangle_it	3.651
r_mcangle_other	3.65
r_scangle_it	2.824
r_scangle_other	2.791
r_mcbond_it	2.042
r_mcbond_other	2.04
r_scbond_it	1.563
r_scbond_other	1.535
r_angle_refined_deg	0.67
r_angle_other_deg	0.259
r_nbd_refined	0.176
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.168
r_symmetry_nbd_refined	0.162
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.156
r_nbd_other	0.141
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.032
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2126
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building