1YRB | pdb_00001yrb

PAB0955 crystal structure : a GTPase in GDP and Mg 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	277	13% PEG4000, 20mM DTT, 10% glycerol, 50mM NaCl, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 0.65mM GDP, 1mM WO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.47	α = 90
b = 85.21	β = 94.61
c = 60.57	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	CCD	ADSC QUANTUM 4	mirror	2004-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.934	ESRF	ID14-2

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	1.75	50	98.6	0.098	0.098	12.47	4.7	60611	59865			27.296

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)
	1.75	1.8	93.5		0.372	0.372	5.91	4	4813

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	1YR6	1.75	15	60500	59763	6086	98.77	0.196	0.196	0.195	0.2	0.247	0.21	RANDOM	33.883

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]
0.23		0.78	-0.76		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.596
r_dihedral_angle_4_deg	16.148
r_dihedral_angle_3_deg	15.387
r_dihedral_angle_1_deg	4.918
r_scangle_it	2.198
r_mcangle_it	1.799
r_scbond_it	1.676
r_angle_refined_deg	1.215
r_mcbond_it	1.107
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.275
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.232
r_metal_ion_refined	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.008
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_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	4216
Nucleic Acid Atoms
Solvent Atoms	381
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
AMoRE	phasing