6ZDC | pdb_00006zdc

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with nickel

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M17

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	292	100 mM MIB buffer, pH 6.0. Protein at 5.5 mg/ml in 50 mM potassium phosphate, 50 mM KCl. 150 nl protein solution and 150 nl reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.467	α = 90
b = 86.535	β = 90
c = 135.916	γ = 90

Symmetry
Space Group	P 2 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		2017-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.25	135.92	98.1	0.2	0.21	0.061	0.994	7	11.4		21876			40.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	84.5		1.872	2.029	0.75	0.345	0.9	6.9

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 (All)	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	5M17	2.251	73.103	21817	1106	97.764	0.179	0.1769	0.19	0.2234	0.23	RANDOM	47.23

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]
-0.734			-2.644		3.378

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.041
r_dihedral_angle_3_deg	15.072
r_dihedral_angle_4_deg	14.786
r_lrange_it	8.161
r_lrange_other	8.116
r_dihedral_angle_1_deg	6.494
r_scangle_it	5.529
r_scangle_other	5.527
r_mcangle_it	5.338
r_mcangle_other	5.337
r_scbond_it	3.47
r_scbond_other	3.469
r_mcbond_it	3.412
r_mcbond_other	3.408
r_angle_other_deg	2.341
r_angle_refined_deg	1.889
r_nbd_other	0.246
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.202
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.134
r_symmetry_xyhbond_nbd_other	0.112
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.035
r_bond_refined_d	0.015
r_gen_planes_other	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2877
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	1

Software

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