7AJK | pdb_00007ajk

Crystal structure of CRYI-B Rac1 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GZL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		279	8% v/v PEG4,000 0.1M Tris pH 8.5 0.2M Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.87	α = 90
b = 81.87	β = 90
c = 355.87	γ = 120

Symmetry
Space Group	P 62 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 EIGER X 16M		2020-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97624	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	59.382	97.92	0.99	18.7	10.6		13493

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.21			0.917

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4GZL	3.1	59.382	13493	672	97.839	0.25	0.2486	0.25	0.2818	0.29	79.88

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]
0.897	0.449		0.897		-2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.659
r_dihedral_angle_4_deg	17.705
r_dihedral_angle_3_deg	17.265
r_lrange_it	14.802
r_lrange_other	14.801
r_scangle_it	11.188
r_scangle_other	11.186
r_mcangle_other	10.795
r_mcangle_it	10.794
r_scbond_it	7.44
r_scbond_other	7.438
r_mcbond_other	7.399
r_mcbond_it	7.398
r_dihedral_angle_1_deg	4.273
r_angle_other_deg	1.128
r_angle_refined_deg	1.087
r_symmetry_nbd_refined	0.499
r_chiral_restr_other	0.395
r_symmetry_xyhbond_nbd_refined	0.277
r_nbd_other	0.275
r_symmetry_nbd_other	0.228
r_nbd_refined	0.209
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.067
r_chiral_restr	0.042
r_symmetry_xyhbond_nbd_other	0.022
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3567
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing