9DHK | pdb_00009dhk

RMI1-RMI2 bound to cyclic peptide L3

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		293	1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 189.15	α = 90
b = 50.622	β = 118.047
c = 181.221	γ = 90

Symmetry
Space Group	C 1 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 EIGER X 16M		2022-11-02	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	2.35	48.272	99.2	0.983	5.6	3.5		63378

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	2.35	2.41			0.406	1.1

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	2.35	48.272	63377	3158	99.047	0.206	0.2035	0.2036	0.2467	0.2475	40.057

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]
-0.362		0.33	-1.142		0.735

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.941
r_dihedral_angle_6_deg	15.875
r_dihedral_angle_2_deg	15.841
r_lrange_it	8.461
r_lrange_other	8.459
r_dihedral_angle_1_deg	7.41
r_scangle_it	6.311
r_scangle_other	6.31
r_scbond_it	4.073
r_scbond_other	4.073
r_mcangle_it	3.951
r_mcangle_other	3.951
r_mcbond_other	2.516
r_mcbond_it	2.515
r_angle_refined_deg	1.941
r_angle_other_deg	0.616
r_nbd_refined	0.223
r_nbd_other	0.213
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.176
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.142
r_ncsr_local_group_4	0.14
r_ncsr_local_group_14	0.13
r_ncsr_local_group_10	0.129
r_ncsr_local_group_16	0.128
r_ncsr_local_group_5	0.124
r_ncsr_local_group_12	0.122
r_ncsr_local_group_18	0.122
r_ncsr_local_group_9	0.112
r_ncsr_local_group_6	0.106
r_ncsr_local_group_17	0.1
r_ncsr_local_group_2	0.099
r_ncsr_local_group_13	0.098
r_ncsr_local_group_11	0.089
r_symmetry_nbtor_other	0.088
r_ncsr_local_group_8	0.085
r_ncsr_local_group_1	0.084
r_ncsr_local_group_3	0.082
r_chiral_restr	0.079
r_ncsr_local_group_7	0.079
r_ncsr_local_group_15	0.051
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9139
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	16

Software

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