1YRA | pdb_00001yra

PAB0955 crystal structure : a GTPase in GDP bound form from Pyrococcus abyssi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	13% PEG 4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 0.65mM GDP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.19	α = 90
b = 84.95	β = 95.07
c = 60.2	γ = 90

Symmetry
Space Group	P 1 21 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	mirror	2004-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.542

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	2.3	50	97.9	0.065	0.065	12.54	3.35	26447	25913			38

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)
	2.3	2.38	96.3		0.348	0.348	3.59	3.3	2468

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 (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	1YR6	2.3	15	26446	25808	2607	97.95	0.19016	0.19016	0.19	0.264	0.2	random	34.923

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]
-0.37		0.72	-0.3		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.466
r_dihedral_angle_4_deg	20.74
r_dihedral_angle_3_deg	18.103
r_dihedral_angle_1_deg	5.734
r_scangle_it	2.301
r_mcangle_it	1.898
r_scbond_it	1.609
r_angle_refined_deg	1.294
r_mcbond_it	1.11
r_nbtor_refined	0.33
r_symmetry_hbond_refined	0.306
r_nbd_refined	0.248
r_xyhbond_nbd_refined	0.235
r_symmetry_vdw_refined	0.227
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4232
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
AMoRE	phasing