5QQG | pdb_00005qqg

PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-541-216

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O33	5O33

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293.15	0.1M bis-tris pH 5.5 24% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.785	α = 90
b = 62.785	β = 90
c = 344.573	γ = 120

Symmetry
Space Group	P 65 2 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 PILATUS 6M		2018-08-03		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.23	54.37	100	0.21	0.217	0.054	0.999	11.2	15.6		20947

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.23	2.35	100		3.115	3.237	0.863	0.333		13.7	2929

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5O33	2.23	57.43	19788	1035	99.97	0.2007	0.197	0.2063	0.2742	0.2744	RANDOM	52.72

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]
0.6	0.3		0.6		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.652
r_dihedral_angle_4_deg	20.896
r_dihedral_angle_3_deg	15.315
r_dihedral_angle_1_deg	6.959
r_mcangle_it	6.297
r_mcbond_it	4.096
r_mcbond_other	4.095
r_angle_refined_deg	1.572
r_angle_other_deg	1.026
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2773
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing