2Q8N | pdb_00002q8n

Crystal structure of Glucose-6-phosphate isomerase (EC 5.3.1.9) (TM1385) from Thermotoga maritima at 1.82 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B0Z	PDB entry 1B0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		273	NANODROP, 0.23M Li Sulfate, 0.10M Tris-HCl, 0.031M HCl, 43% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.506	α = 90
b = 125.867	β = 90
c = 245.476	γ = 90

Symmetry
Space Group	I 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2005-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.00000	SSRL	BL9-2

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	1.82	45.932	99.8	0.052	19.96	7.9		161864		-3	35.51

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)
	1.82	1.89	99.9		0.666	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1B0Z	1.82	45.932	161863	8195	99.84	0.199	0.197	0.2	0.237	0.24	RANDOM	37.431

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]
4.31			-1.89		-2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.453
r_dihedral_angle_4_deg	18.151
r_dihedral_angle_3_deg	14.371
r_scangle_it	7.229
r_dihedral_angle_1_deg	5.945
r_scbond_it	5.182
r_mcangle_it	2.989
r_mcbond_it	1.962
r_angle_refined_deg	1.607
r_angle_other_deg	0.994
r_mcbond_other	0.406
r_symmetry_vdw_other	0.264
r_nbd_refined	0.214
r_nbd_other	0.197
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.129
r_chiral_restr	0.097
r_nbtor_other	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10624
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOLREP	phasing