7EAP | pdb_00007eap

Crystal structure of IpeA-XXXG complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5YOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Bis-Tris pH 5.5, 2.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.197	α = 90
b = 94.197	β = 90
c = 189.003	γ = 120

Symmetry
Space Group	P 31 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	90	PIXEL	DECTRIS EIGER X 16M		2018-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.42	47.12	99.7	0.995	10.4	10.1		181988

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.47			0.876

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	THROUGHOUT	5YOT	1.42	29.48	172870	9099	99.7	0.1195	0.118	0.1181	0.1469	0.1467	RANDOM	20.214

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]
0.1	0.05		0.1		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.853
r_dihedral_angle_4_deg	15.116
r_dihedral_angle_3_deg	12.183
r_dihedral_angle_1_deg	6.757
r_rigid_bond_restr	4.6
r_angle_refined_deg	2.11
r_angle_other_deg	1.664
r_chiral_restr	0.128
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5836
Nucleic Acid Atoms
Solvent Atoms	603
Heterogen Atoms	205

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing