4CD7 | pdb_00004cd7

The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG and beta-1,4-mannobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CIV	PDB ENTRY 3CIV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		0.1 M SODIUM ACETATE PH 4.6, 4% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.52	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.472	α = 90
b = 76.586	β = 90
c = 140.212	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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2013-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	1.65	76.59	97.9	0.16	6.7	6.3		88667		2

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	1.65	1.68	78.3		0.63	1.8	4.7

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	PDB ENTRY 3CIV	1.65	70.11	83793	4466	97.32	0.15313	0.15081	0.17	0.19617	0.21	RANDOM	15.621

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]
-0.4			0.6		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	30.61
r_dihedral_angle_2_deg	28.686
r_dihedral_angle_4_deg	15.523
r_dihedral_angle_3_deg	12.606
r_sphericity_bonded	8.839
r_dihedral_angle_1_deg	6.118
r_scangle_it	3.341
r_scbond_it	2.773
r_rigid_bond_restr	2.466
r_mcangle_it	2.357
r_mcbond_it	1.975
r_mcbond_other	1.975
r_angle_refined_deg	1.405
r_angle_other_deg	1.03
r_symmetry_vdw_refined	0.344
r_nbd_refined	0.244
r_symmetry_vdw_other	0.192
r_nbtor_refined	0.185
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.106
r_xyhbond_nbd_other	0.089
r_nbtor_other	0.087
r_symmetry_hbond_refined	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4971
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing