8I85

Crystal structure of Cph001-D189N in complex with ATP

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
2.53	51.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.829	α = 90
b = 85.171	β = 90
c = 87.344	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	100	CCD	RAYONIX MX300HE		2022-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1	NSRRC	BL15A1

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	2.17	30	99.5	0.045	41.1	7.3		33181

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	2.17	2.26	95.5		0.406	4.8	7.3

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	2.17	28.35	30137	2552	98.56	0.20105	0.19654	0.25492	RANDOM	33.654

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]
-0.03			0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.704
r_dihedral_angle_1_deg	6.296
r_dihedral_angle_2_deg	5.834
r_long_range_B_refined	5.158
r_long_range_B_other	5.111
r_scangle_other	3.002
r_mcangle_it	2.847
r_mcangle_other	2.846
r_scbond_it	1.795
r_scbond_other	1.794
r_mcbond_it	1.669
r_mcbond_other	1.666
r_angle_refined_deg	0.926
r_angle_other_deg	0.449
r_chiral_restr	0.041
r_bond_other_d	0.009
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
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	4223
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	56

Software

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