3Q88 | pdb_00003q88

Glucose-6-phosphate isomerase from Francisella tularensis complexed with ribose 1,5-bisphosphate.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LJK	PDB entry 3LJK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	0.2 M Ca(OAc)2, 0.1 M MES buffer, 10% 2-propanol, 0.01 M 5-phospho-alpha-D-ribose 1-diphosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.465	α = 90
b = 114.465	β = 90
c = 84.5	γ = 120

Symmetry
Space Group	P 32 2 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 315		2010-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	1.7	34	100	0.108	10.1	8.2	70571	70571			33

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)
	1.7	1.73	100		0.822	2.69	7.7	3489

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	PDB entry 3LJK	1.7	33.99	70373	70373	3521	99.66	0.1476	0.1476	0.1462	0.15	0.1739	0.17	RANDOM	27.076

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]
-0.47	-0.24		-0.47		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.266
r_dihedral_angle_4_deg	16.309
r_dihedral_angle_3_deg	15.047
r_dihedral_angle_1_deg	5.797
r_scangle_it	4.345
r_scbond_it	2.652
r_mcangle_it	1.697
r_angle_refined_deg	1.695
r_angle_other_deg	0.994
r_mcbond_it	0.982

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.266
r_dihedral_angle_4_deg	16.309
r_dihedral_angle_3_deg	15.047
r_dihedral_angle_1_deg	5.797
r_scangle_it	4.345
r_scbond_it	2.652
r_mcangle_it	1.697
r_angle_refined_deg	1.695
r_angle_other_deg	0.994
r_mcbond_it	0.982
r_mcbond_other	0.32
r_chiral_restr	0.111
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4312
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

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.