1XFG | pdb_00001xfg

Glutaminase domain of glucosamine 6-phosphate synthase complexed with l-glu hydroxamate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	0.1 M cacodylate, 1 M sodium acetate, 20% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.25	α = 90
b = 82.4	β = 90
c = 85.83	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	295	IMAGE PLATE	MARRESEARCH	MIRROR	1993-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9300	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.85	15	99.6	0.053	15.2	4.4	42930	42930		-3	18.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.9	92.3		0.262	3.2	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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	none used	1GPH	1.85	15	42930	42930		99.6	0.159	0.159	0.159	0.16		26.6

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]
1.11			-0.72		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.984
r_scangle_it	12.947
r_dihedral_angle_1_deg	11.45
r_scbond_it	10.125
r_mcangle_it	7.256
r_mcbond_it	5.026
r_angle_refined_deg	1.83
r_nbtor_refined	0.331
r_nbd_refined	0.246
r_symmetry_vdw_refined	0.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.984
r_scangle_it	12.947
r_dihedral_angle_1_deg	11.45
r_scbond_it	10.125
r_mcangle_it	7.256
r_mcbond_it	5.026
r_angle_refined_deg	1.83
r_nbtor_refined	0.331
r_nbd_refined	0.246
r_symmetry_vdw_refined	0.209
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.127
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3695
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.