2HXS | pdb_00002hxs

Crystal Structure of Rab28A GTPase in the Inactive (GDP-3'P-Bound) Form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YZK	PDB ENTRY 1YZK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	20% PEG 3360, 100 mM NaCl, 100 mM Potassium Acetate, 5% glycerol, 20 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.51	α = 90
b = 56.621	β = 90
c = 85.109	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR scanner 345 mm plate			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.1	31	98.3	0.075	0.075	24.7	8.3	59785	58782	1	1	11.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.1	1.14	96.8		0.367	0.367	4.25	5.1	5607

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YZK	1.1	31	57639	55034	2945	95.48	0.152	0.152	0.14867	0.15	0.1836	0.18	RANDOM	18.885

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]
0.98			0.06		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.25
r_dihedral_angle_4_deg	15.846
r_dihedral_angle_3_deg	12.531
r_sphericity_free	11.829
r_sphericity_bonded	6.65
r_scangle_it	5.905
r_dihedral_angle_1_deg	5.268
r_scbond_it	4.531
r_mcangle_it	3.513
r_rigid_bond_restr	2.67
r_mcbond_it	2.618
r_angle_refined_deg	2.184
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.251
r_nbd_refined	0.233
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.139
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1503
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing