8I84

Crystal structure of Cph001-D189N in complex with CMN IIB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8I80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	Sodium acetate trihydrate, Polyethylene glycol 4,000, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.755	α = 90
b = 85.153	β = 90
c = 86.815	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	277	CCD	RAYONIX MX300-HS		2022-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	30	99	0.071	25.5	7.6		31648

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	92.9		0.445	2.9	6.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	23.93	25737	1265	84.36	0.21404	0.21158	0.26736	RANDOM	35.468

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]
-0.07			0.1		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.643
r_dihedral_angle_2_deg	6.632
r_dihedral_angle_1_deg	6.392
r_long_range_B_refined	5.587
r_long_range_B_other	5.586
r_scangle_other	3.227
r_mcangle_it	3.153
r_mcangle_other	3.152
r_scbond_it	1.925
r_scbond_other	1.925
r_mcbond_it	1.875
r_mcbond_other	1.875
r_angle_refined_deg	0.981
r_angle_other_deg	0.79
r_chiral_restr	0.043
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4255
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	15

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
HKL-2000	data reduction
MOLREP	phasing