5QQM | pdb_00005qqm

PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-565-325

X-RAY DIFFRACTION

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
2.35	47.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.498	α = 90
b = 62.498	β = 90
c = 342.286	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	2.02	342.41	100	0.342	0.348	0.059	0.946	10.8	34.6		27501

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.08	100		3.64	3.759	0.908		17.7	2053

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	2.02	57.05	25975	1359	99.78	0.2143	0.2113	0.22	0.2731	0.28	RANDOM	37.948

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]
1.46	0.73		1.46		-4.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.25
r_dihedral_angle_4_deg	24.478
r_dihedral_angle_3_deg	14.418
r_dihedral_angle_1_deg	6.856
r_mcangle_it	4.801
r_mcbond_it	3.234
r_mcbond_other	3.233
r_angle_refined_deg	1.804
r_angle_other_deg	1.093
r_chiral_restr	0.118

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.25
r_dihedral_angle_4_deg	24.478
r_dihedral_angle_3_deg	14.418
r_dihedral_angle_1_deg	6.856
r_mcangle_it	4.801
r_mcbond_it	3.234
r_mcbond_other	3.233
r_angle_refined_deg	1.804
r_angle_other_deg	1.093
r_chiral_restr	0.118
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
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	26

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.