8JQU

Crystal structure of GppNHp bound GTPase domain of Rab5a from Leishmania donovani

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.2M Magnesium Acetate, 0.1M Tris-HCl pH 8.5, 19% PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.552	α = 90
b = 42.266	β = 103.387
c = 37.777	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2023-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.798	35	99.7	0.054	25	6.6		15882

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	1.8	1.86	97.7		0.22	0.242	0.1	0.975		5.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.798	27.354	15882	793	99.449	0.164	0.1616	0.2029	26.533

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]
0.04		0.248	0.152		-0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.582
r_dihedral_angle_4_deg	17.837
r_dihedral_angle_3_deg	14.703
r_lrange_it	7.142
r_dihedral_angle_1_deg	6.267
r_scangle_it	5.104
r_mcangle_it	3.901
r_scbond_it	3.385
r_mcbond_it	2.553
r_angle_refined_deg	2.13
r_nbtor_refined	0.317
r_nbd_refined	0.239
r_symmetry_nbd_refined	0.18
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.157
r_chiral_restr	0.153
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_metal_ion_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1235
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	37

Software

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