7BTD | pdb_00007btd

Crystal structure of Rheb Y35N mutant bound to GppNHp

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	290	0.2 M Ammonium acetate: 0.1 M HEPES, pH 7.5: 25% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.637	α = 90
b = 102.962	β = 90
c = 47.715	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS3 S 6M		2018-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9785	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2	50.01	99.8	0.1	0.108	0.04	4.6	7.1		16650

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	2	2.07	99.1		0.547	0.596	0.232	0.9		6.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	1XTS	2	50	15789	833	99.75	0.168	0.1661	0.1663	0.2083	0.2082	RANDOM	38.068

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]
0.44			0.35		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.446
r_sphericity_bonded	16.121
r_sphericity_free	14.664
r_dihedral_angle_3_deg	14.518
r_dihedral_angle_1_deg	6.117
r_dihedral_angle_4_deg	4.415
r_rigid_bond_restr	1.41
r_angle_refined_deg	1.217
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1340
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing