6ZDF | pdb_00006zdf

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	1 M sodium succinate pH 7.0, 1% w/v PEG-MME2000 Protein at 10 mg/ml in buffer: 25 mM HEPES pH 7.0, 200 mM NaCl 100 nl protein solution and 200 nl reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.245	α = 90
b = 144.245	β = 90
c = 139.661	γ = 90

Symmetry
Space Group	P 43 21 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		2017-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	3	102.205	100	0.582	0.611	0.135	0.974	5	20.3		30161			41.75

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	3	3.16	99.8		1.175	1.205	0.265	0.253	2.9	20.5

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	6ZDC	3	102.205	30099	1429	99.947	0.218	0.2153	0.22	0.2687	0.27	RANDOM	49.027

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]
0.31			0.31		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.265
r_dihedral_angle_3_deg	19.232
r_dihedral_angle_4_deg	17.66
r_lrange_it	7.502
r_dihedral_angle_1_deg	5.968
r_scangle_it	4.687
r_mcangle_it	4.566
r_scbond_it	2.899
r_mcbond_it	2.769
r_angle_refined_deg	1.7
r_nbtor_refined	0.298
r_symmetry_xyhbond_nbd_refined	0.249
r_symmetry_nbd_refined	0.205
r_nbd_refined	0.18
r_chiral_restr	0.126
r_xyhbond_nbd_refined	0.11
r_ncsr_local_group_2	0.085
r_ncsr_local_group_1	0.082
r_ncsr_local_group_3	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8853
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	45

Software

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