9LBF | pdb_00009lbf

The crystal structure of the truncated PAK2 containing D368N mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1M DL-malic acid pH5.51, 1.4M (NH4)2SO4, 0.025% CH2Cl2

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.325	α = 90
b = 167.325	β = 90
c = 212.863	γ = 120

Symmetry
Space Group	H 3 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		2018-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.987	SSRF	BL19U1

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	2.62	50	100	0.159	0.983	14.3	10.9		34739

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	2.62	2.71	100		1.245	0.815	2	11

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	2.62	42.89	30996	1470	89.092	0.199	0.1983	0.2036	0.222	0.2246	55.592

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]
-0.23	-0.115		-0.23		0.746

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	16.331
r_lrange_it	16.319
r_dihedral_angle_6_deg	15.234
r_dihedral_angle_3_deg	14.109
r_scangle_it	11.07
r_scangle_other	10.975
r_mcangle_it	10.254
r_mcangle_other	10.254
r_scbond_it	6.879
r_scbond_other	6.788
r_dihedral_angle_1_deg	6.726
r_mcbond_it	6.556
r_mcbond_other	6.556
r_angle_refined_deg	1.614
r_dihedral_angle_2_deg	0.905
r_angle_other_deg	0.539
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_other	0.214
r_nbd_refined	0.197
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.167
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_other	0.115
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.008
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	5292
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing