Experiment: 7PE0

Crystal structure of IpgC in complex with J52

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SCB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		299	30 % PEG 4000, 0.1 M TRIS pH 7.0, 0.3 M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.642	α = 90
b = 57.642	β = 90
c = 159.612	γ = 120

Symmetry
Space Group	P 32 2 1

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		2020-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.5	47.64	99.9	0.054	1	19.78	10.7		50323

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58			0.879	0.873	2.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6scb	1.5	47.64	47701	2621	99.85	0.1743	0.1736	0.1728	0.185	0.181	RANDOM	29.19

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]
21.44			21.44		-42.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.014
r_dihedral_angle_3_deg	12.103
r_dihedral_angle_4_deg	11.449
r_dihedral_angle_1_deg	4.55
r_angle_refined_deg	1.233
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2119
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	18

Software

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