4V17 | pdb_00004v17

Structure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SEMET DERIVATIVE FROM 2.28 A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		1.2 M NA2 CITRATE, 0.1 M HEPES PH 7.5 CRYO 30% GLYCEROL IN ABOVE CONDITION

Crystal Properties
Matthews coefficient	Solvent content
2.57	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.093	α = 90
b = 131.093	β = 90
c = 105.199	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	30.17	100	0.12	12.5	16.9		26385

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	2.05	100		1.5	1.7	15.2

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	SEMET DERIVATIVE FROM 2.28 A	2	77.16	22333	1200	99.76	0.20403	0.20269	0.21	0.22875	0.24	RANDOM	57.336

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]
0.95	0.48		0.95		-3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.534
r_dihedral_angle_3_deg	14.216
r_dihedral_angle_1_deg	6.849
r_mcangle_it	4.084
r_scbond_it	3.705
r_mcbond_it	2.662
r_mcbond_other	2.662
r_angle_refined_deg	1.263
r_angle_other_deg	0.868
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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	2289
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing