6RRX | pdb_00006rrx

GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-3-piperidinol

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M sodium succinate, pH 7.4 10 % PEG 3350 with microseeding

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.005	α = 90
b = 91.377	β = 90
c = 132.527	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 EIGER X 16M		2019-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.84	75.34	100	0.998	13.2	8.1		94351

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.87	100		0.75	1.2	8

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	3bub	1.84	75.34	89577	4689	99.95	0.203	0.2002	0.21	0.2563	0.26	RANDOM	41.18

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]
-3.41			4.94		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.01
r_dihedral_angle_4_deg	17.656
r_dihedral_angle_3_deg	15.317
r_dihedral_angle_1_deg	7.433
r_mcangle_it	4.391
r_mcbond_it	3.139
r_mcbond_other	3.138
r_angle_other_deg	2.327
r_angle_refined_deg	1.514
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.01
r_dihedral_angle_4_deg	17.656
r_dihedral_angle_3_deg	15.317
r_dihedral_angle_1_deg	7.433
r_mcangle_it	4.391
r_mcbond_it	3.139
r_mcbond_other	3.138
r_angle_other_deg	2.327
r_angle_refined_deg	1.514
r_chiral_restr	0.071
r_bond_other_d	0.035
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8031
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.