4AYO | pdb_00004ayo

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.98	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.77	α = 90
b = 143.77	β = 90
c = 50.155	γ = 120

Symmetry
Space Group	H 3

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	2011-05-14	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	0.85	46.52	91.9	0.04	17.9	5.2		312602		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	0.85	0.9	63.4		0.39	2.6	2.6

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 1NXC	0.85	46.57	296806	15793	91.88	0.09515	0.09464	0.1066	0.10478	0.1156	RANDOM	7.363

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			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.952
r_sphericity_free	28.712
r_dihedral_angle_4_deg	14.851
r_dihedral_angle_3_deg	11.393
r_dihedral_angle_1_deg	6.144
r_sphericity_bonded	5.501
r_rigid_bond_restr	1.621
r_angle_refined_deg	1.404
r_symmetry_hbond_refined	0.973
r_angle_other_deg	0.786
r_symmetry_hbond_other	0.338
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.258
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.168
r_symmetry_vdw_other	0.16
r_chiral_restr	0.085
r_nbtor_other	0.085
r_xyhbond_nbd_other	0.076
r_metal_ion_refined	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	3451
Nucleic Acid Atoms
Solvent Atoms	817
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing