2W90

Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZI0	PDB ENTRY 2ZI0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		0.2 M LISO4, 2.2 M (NH4)2SO4, pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.95	α = 90
b = 119.5	β = 90
c = 142.24	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 CCD	TORODIAL FOCUSING MIRROR	2007-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.2	50	99.4	0.12	10.43	6.28		57708

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	2.2	2.25	99.6		0.59	3.63	6.22

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZI0	2.2	71.07	55339	2947	99.3	0.174	0.171	0.234	RANDOM	32.58

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]
1.74			-2.8		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.937
r_dihedral_angle_4_deg	17.411
r_dihedral_angle_3_deg	16.318
r_dihedral_angle_1_deg	5.43
r_scangle_it	2.733
r_scbond_it	2.043
r_angle_refined_deg	1.278
r_mcangle_it	1.164
r_angle_other_deg	0.916
r_mcbond_it	0.912
r_symmetry_vdw_other	0.238
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.201
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.181
r_mcbond_other	0.177
r_symmetry_hbond_refined	0.175
r_nbtor_other	0.087
r_chiral_restr	0.076
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.012
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_symmetry_hbond_other	0.003
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7344
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing