9DI4 | pdb_00009di4

RMI1-RMI2 bound to cyclic peptide L4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	293	0.01M zinc chloride, 0.1M sodium acetate pH 5.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.298	α = 90
b = 136.298	β = 90
c = 88.608	γ = 120

Symmetry
Space Group	P 64 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 EIGER X 16M		2022-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2.69	49.169	99.6	0.999	22.2	38.8		13881

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	2.69	2.83			0.894

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	2.696	49.169	13858	673	99.77	0.173	0.1693	0.1719	0.2482	0.2506	61.815

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]
-3.401	-1.701		-3.401		11.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21
r_dihedral_angle_3_deg	17.726
r_dihedral_angle_6_deg	16.483
r_lrange_other	15.019
r_lrange_it	15.018
r_scangle_it	14.219
r_scangle_other	14.215
r_scbond_it	10.732
r_scbond_other	10.728
r_mcangle_it	9.794
r_mcangle_other	9.784
r_dihedral_angle_1_deg	7.959
r_mcbond_it	7.644
r_mcbond_other	7.636
r_angle_refined_deg	2.979
r_angle_other_deg	0.934
r_nbd_refined	0.235
r_symmetry_nbd_other	0.213
r_nbtor_refined	0.198
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_refined	0.156
r_nbd_other	0.151
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.104
r_symmetry_xyhbond_nbd_refined	0.034
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2281
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	2

Software

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