2IPN

Crystal structure of a disulfide mutant glucose binding protein

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	20% PEG 6000, 50mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.305	α = 90
b = 36.586	β = 106.92
c = 65.029	γ = 90

Symmetry
Space Group	P 1 21 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 4		2006-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

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	1.15	50	99.5	0.063	11.8	3.3	97506	97506

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)
	1.15	1.19	97.9		0.284	3.3	2.5	9495

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HPH	1.15	50	97478	97478	4875	99.41	0.153	0.153	0.153	0.168	RANDOM	7.754

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]
		0.07	0.12		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.111
r_dihedral_angle_3_deg	11.226
r_dihedral_angle_4_deg	8.562
r_dihedral_angle_1_deg	5.371
r_sphericity_free	3.803
r_scangle_it	2.555
r_sphericity_bonded	2.079
r_scbond_it	1.777
r_mcangle_it	1.25
r_angle_refined_deg	1.244
r_angle_other_deg	0.881
r_mcbond_it	0.873
r_rigid_bond_restr	0.788
r_mcbond_other	0.333
r_symmetry_vdw_other	0.231
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.215
r_nbd_other	0.175
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.113
r_metal_ion_refined	0.087
r_nbtor_other	0.085
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2469
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
AMoRE	phasing