4CD8 | pdb_00004cd8

The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManMIm

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
2.06	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.82	α = 90
b = 75.89	β = 90
c = 91.48	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	2012-09-28	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	1.47	58.41	99.7	0.06	14	6.3		52176		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	1.47	1.51	99		0.71	2.6	6.2

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	PDB ENTRY 3CIV	1.47	58.41	49455	2659	99.67	0.17274	0.17043	0.18	0.21511	0.23	RANDOM	21.867

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]
3.04			-3.58		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.384
r_rigid_bond_restr	27.306
r_sphericity_free	23.15
r_sphericity_bonded	15.67
r_dihedral_angle_4_deg	13.583
r_dihedral_angle_3_deg	12.195
r_dihedral_angle_1_deg	6.41
r_scangle_it	4.262
r_scbond_it	3.962
r_mcangle_it	3.423
r_mcbond_it	2.972
r_mcbond_other	2.958
r_angle_refined_deg	1.508
r_angle_other_deg	0.834
r_symmetry_vdw_refined	0.297
r_symmetry_vdw_other	0.264
r_nbd_refined	0.24
r_symmetry_hbond_refined	0.2
r_nbtor_refined	0.192
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.09
r_nbtor_other	0.083
r_xyhbond_nbd_other	0.06
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	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	2453
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	25

Software

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