2HPH

High resolution structure of E. coli glucose/galactose binding protein bound with glucose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	20% PEG6000, 50mM NaHEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.26	α = 90
b = 36.58	β = 107.19
c = 64.94	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	MAR CCD 165 mm		2003-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.90	APS	22-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	1.33	25	98.3	0.161	5.22		62566	62566		-3	14.341

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)
	1.33	1.5	94.9	89.2	0.343	3.18		18133

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	2GBP	1.33	24.57	62566	62564	3129	100	0.155	0.155	0.154	0.178	RANDOM	6.717

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]
-0.01		0.12	0.44		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.852
r_dihedral_angle_3_deg	11.546
r_dihedral_angle_4_deg	10.104
r_dihedral_angle_1_deg	5.468
r_sphericity_free	4.482
r_scangle_it	3.059
r_scbond_it	2.185
r_sphericity_bonded	1.984
r_mcangle_it	1.437
r_angle_refined_deg	1.3
r_mcbond_it	1.083
r_rigid_bond_restr	1.001
r_angle_other_deg	0.881
r_mcbond_other	0.385
r_symmetry_vdw_refined	0.286
r_nbd_refined	0.225
r_nbd_other	0.18
r_nbtor_refined	0.175
r_symmetry_vdw_other	0.169
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.113
r_nbtor_other	0.085
r_chiral_restr	0.083
r_metal_ion_refined	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2388
Nucleic Acid Atoms
Solvent Atoms	523
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
AMoRE	phasing