9D53 | pdb_00009d53

PAK4 in complex with compound 7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XBU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Bis-Tris-Propane, pH 9.0, 10% PEG 20,000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.703	α = 90
b = 62.703	β = 90
c = 149.792	γ = 90

Symmetry
Space Group	P 41 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 PILATUS3 6M		2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

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	2.468	50	99.9	0.91	13.07	15.9		11390

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	2.468	2.62			0.91	1.45

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	2.468	48.124	11311	554	99.298	0.19	0.1858	0.1934	0.2627	0.2617	70.605

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]
1.806			1.806		-3.613

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.975
r_dihedral_angle_2_deg	14.941
r_dihedral_angle_6_deg	13.863
r_lrange_it	10.559
r_lrange_other	10.557
r_scangle_it	8.733
r_scangle_other	8.73
r_dihedral_angle_1_deg	7.916
r_mcangle_it	7.115
r_mcangle_other	7.112
r_scbond_it	5.927
r_scbond_other	5.927
r_mcbond_it	5.027
r_mcbond_other	5.011
r_angle_refined_deg	1.712
r_angle_other_deg	0.546
r_nbd_refined	0.236
r_symmetry_nbd_other	0.21
r_nbd_other	0.209
r_symmetry_nbd_refined	0.196
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2293
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	24

Software

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