1UY1

Binding sub-site dissection of a family 6 carbohydrate-binding module by X-ray crystallography and isothermal titration calorimetry

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GMM	PDB ENTRY 1GMM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		pH 4.50

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.438	α = 90
b = 83.438	β = 90
c = 44.776	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU R-AXIS IV++	OSMIC BLUE		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002

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	1.8	20	99.9	0.068	16.3	8.2		15153

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	1.8	1.86	100		0.336	5.6	7.8

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 1GMM	1.8	20	14366	767	99.9	0.14	0.138	0.178	RANDOM	23.41

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]
-0.65			-0.65		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.063
r_scangle_it	6.336
r_scbond_it	4.437
r_mcangle_it	2.644
r_mcbond_it	1.759
r_angle_refined_deg	1.622
r_angle_other_deg	0.89
r_symmetry_hbond_refined	0.302
r_symmetry_vdw_other	0.267
r_nbd_other	0.262
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.196
r_metal_ion_refined	0.172
r_chiral_restr	0.11
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_other	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	986
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing