8WZD | pdb_00008wzd

The Crystal Structure of PKCi from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M Na2tartrate, 0.1M Hepes pH7.0, 20% SOKALAN PA25 CL

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.76	α = 90
b = 75.047	β = 90
c = 80.266	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	PIXEL	DECTRIS PILATUS3 6M		2021-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.1806	CLSI	08ID-1

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	2.05	45.76	100	0.149	9.9	6.4		17997

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	2.05	2.11			0.942

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	2.05	40.165	17948	1014	99.939	0.173	0.1705	0.18	0.2172	0.22	28.127

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]
-2.26			3.639		-1.378

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.664
r_dihedral_angle_3_deg	13.92
r_dihedral_angle_1_deg	6.523
r_lrange_it	5.878
r_lrange_other	5.778
r_dihedral_angle_2_deg	5.295
r_scangle_it	4.647
r_scangle_other	4.645
r_scbond_it	3.25
r_scbond_other	3.249
r_mcangle_it	2.952
r_mcangle_other	2.951
r_mcbond_other	2.122
r_mcbond_it	2.121
r_angle_refined_deg	1.385
r_angle_other_deg	0.453
r_nbd_refined	0.194
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.167
r_nbd_other	0.166
r_symmetry_nbd_refined	0.133
r_ncsr_local_group_1	0.117
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.011
r_bond_refined_d	0.007
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	1779
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

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