9LBG | pdb_00009lbg

The crystal structure of the truncated PAK2 containing K278R 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 pH5.50, 1.3M (NH4)2SO4,3% methanol

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.935	α = 90
b = 166.935	β = 90
c = 208.988	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 EIGER X 16M		2018-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

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	2.89	50	99.8	0.102	0.997	17.2	8.6		24956

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	2.89	3	99.9		1.356	0.789	2	8.7

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	2.89	49.137	24956	1251	98.636	0.197	0.1948	0.1959	0.2327	0.2283	102.698

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]
-3.705	-1.852		-3.705		12.018

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	25.686
r_lrange_other	25.686
r_scangle_it	21.486
r_scangle_other	21.481
r_mcangle_it	19.865
r_mcangle_other	19.863
r_dihedral_angle_6_deg	17.252
r_scbond_it	15.404
r_scbond_other	15.389
r_dihedral_angle_3_deg	15.337
r_mcbond_it	14.506
r_mcbond_other	14.497
r_dihedral_angle_2_deg	7.03
r_dihedral_angle_1_deg	6.686
r_angle_refined_deg	1.69
r_angle_other_deg	0.526
r_symmetry_xyhbond_nbd_refined	0.391
r_nbd_other	0.26
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.204
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.086
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.01
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	5402
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	14

Software

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