6YUM | pdb_00006yum

CK2 alpha bound to unclosed Macrocycle

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PE2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES pH 6.5 0.2 ammonia sulphate 30% PEG 5000 MME 10 mg/mL protein

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.479	α = 90
b = 125.479	β = 90
c = 124.655	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS 2M-F		2018-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000031	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.75	44.36	99.9	0.045	0.998	10.5	9.6		26481

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.9	99.9		0.316	0.923

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3PE2	2.75	44.36	26427	1407	99.789	0.264	0.2626	0.26	0.2838	0.28	68.329

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]
-0.185			-0.185		0.371

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.055
r_dihedral_angle_3_deg	16.246
r_dihedral_angle_4_deg	13.493
r_lrange_it	7.686
r_lrange_other	7.686
r_dihedral_angle_1_deg	6.725
r_mcangle_it	3.783
r_mcangle_other	3.783
r_scangle_it	3.387
r_scangle_other	3.386
r_mcbond_it	2.234
r_mcbond_other	2.232
r_scbond_it	1.935
r_scbond_other	1.934
r_angle_other_deg	1.5
r_angle_refined_deg	1.376
r_nbd_refined	0.219
r_nbd_other	0.211
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.175
r_xyhbond_nbd_refined	0.121
r_symmetry_nbd_refined	0.112
r_ncsr_local_group_1	0.096
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.079
r_ext_dist_refined_d	0.044
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5323
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	96

Software

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