9N2R | pdb_00009n2r

Structure of GTP-bound GM4951

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1M succinic acid pH 7.0, 0.1 M HEPES pH 7.0, and 1% (wt/vol) PEG-MME 2000

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.759	α = 92.31
b = 100.245	β = 101.24
c = 152.347	γ = 89.86

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2022-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	2.754	46.02	88.1	0.979	11.4	4.4		78604

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	2.754	2.8			0.669

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 (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	2.75	46.02	57883	3116	68	0.21062	0.20867	0.2132	0.24659	0.2502	RANDOM	54.965

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]
0.07	0.03	-0.03	0.02	-0.05	-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.866
r_long_range_B_refined	13.867
r_long_range_B_other	13.867
r_dihedral_angle_2_deg	13.468
r_scangle_other	7.203
r_mcangle_it	6.87
r_mcangle_other	6.87
r_dihedral_angle_1_deg	6
r_scbond_other	4.438
r_scbond_it	4.437
r_mcbond_it	4.231
r_mcbond_other	4.231
r_angle_refined_deg	1.363
r_angle_other_deg	0.535
r_chiral_restr	0.065
r_bond_other_d	0.019
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19124
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	296

Software

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