2B8W | pdb_00002b8w

Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP/AlF4

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F5N	PDB ENTRY 1F5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			298	5% PEG3350, 150 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.617	α = 90
b = 101.927	β = 90
c = 54.121	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	CCD	ADSC QUANTUM 4		2002-06-15	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.22	30	98.4	0.078	20.6	14.05		41099		-3	38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.25	97.7		0.485	5.5	13.4

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	PDB ENTRY 1F5N	2.22	29.75	38814	38814	2758	99.6	0.193	0.19	0.2	0.233	0.24	RANDOM	31.22

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]
-1.36			-0.76		2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.297
r_dihedral_angle_4_deg	24.582
r_dihedral_angle_3_deg	20.79
r_dihedral_angle_1_deg	8.735
r_scangle_it	6.814
r_scbond_it	5.09
r_mcangle_it	3.057
r_mcbond_it	2.39
r_angle_refined_deg	0.781
r_nbtor_refined	0.323
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.067
r_gen_planes_refined	0.03
r_bond_refined_d	0.007
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_refined
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	4582
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing