9D51 | pdb_00009d51

Structure of PAK2 in complex with compound 12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DEW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% (w/v) PEG 3350, 200 mM Ammonium tartrate dibasic

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.629	α = 90
b = 80.755	β = 106.186
c = 66.742	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 9M		2021-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	47.783	98.6	0.091	0.996	7.4	7.5		36183

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	98.4		1.405	0.657	0.8	7.7

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	2.1	47.783	36165	1790	98.349	0.215	0.2117	0.215	0.2855	0.2843	72.645

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]
-0.441		-0.511	-0.567		1.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.429
r_dihedral_angle_2_deg	16.352
r_dihedral_angle_6_deg	15.78
r_lrange_other	12.19
r_lrange_it	12.168
r_scangle_other	10.39
r_scangle_it	10.377
r_mcangle_it	9.282
r_mcangle_other	9.281
r_dihedral_angle_1_deg	8.387
r_scbond_it	8.008
r_scbond_other	7.983
r_mcbond_it	7.467
r_mcbond_other	7.464
r_angle_refined_deg	2.592
r_angle_other_deg	0.817
r_symmetry_xyhbond_nbd_refined	0.338
r_nbd_refined	0.225
r_ncsr_local_group_1	0.224
r_symmetry_nbd_other	0.217
r_nbd_other	0.215
r_xyhbond_nbd_refined	0.209
r_nbtor_refined	0.19
r_symmetry_nbd_refined	0.129
r_chiral_restr	0.123
r_symmetry_nbtor_other	0.094
r_symmetry_xyhbond_nbd_other	0.066
r_bond_refined_d	0.014
r_chiral_restr_other	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4510
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	50

Software

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