9S9T | pdb_00009s9t

Structure of human PKCBeta Kinase domain with Ruboxistaurin, D427N mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.17	293	0.1M Citrate pH 5.17 12.3% PEG 6k

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.327	α = 90
b = 102.327	β = 90
c = 82.827	γ = 120

Symmetry
Space Group	P 31 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 EIGER2 XE CdTe 9M		2022-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.67	Diamond	I24

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	3.42	60.511	100	0.995	3.8	20		7021

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	3.42	3.47			0.175	0.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.425	60.511	7006	364	99.829	0.218	0.2142	0.2146	0.2897	0.2909	144.059

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]
-0.507	-0.253		-0.507		1.644

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	23.781
r_lrange_other	23.78
r_dihedral_angle_2_deg	23.658
r_dihedral_angle_3_deg	19.657
r_scangle_it	18.913
r_scangle_other	18.908
r_mcangle_it	16.524
r_mcangle_other	16.519
r_dihedral_angle_6_deg	16.006
r_scbond_it	12.54
r_scbond_other	12.535
r_mcbond_it	10.809
r_mcbond_other	10.8
r_dihedral_angle_1_deg	7.458
r_angle_refined_deg	2.193
r_angle_other_deg	1.059
r_nbd_refined	0.192
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.163
r_symmetry_nbd_other	0.139
r_chiral_restr	0.105
r_xyhbond_nbd_refined	0.101
r_nbd_other	0.1
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_refined	0.042
r_gen_planes_refined	0.012
r_bond_refined_d	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2529
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
gemmi	data extraction
DIALS	data scaling
MrBUMP	phasing
PHASER	phasing