5C1E

Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.6	294	Protein (6.5 mg/mL) in 50-100 mM acetate buffer mixed 1:1 with 1.9 M ammonium sulfate, 100 mM sodium acetate, pH 3.6

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.614	α = 90
b = 113.543	β = 90
c = 88.765	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	123	IMAGE PLATE	RIGAKU RAXIS IV++	AXCo PX70 QUARTZ GLASS CAPILLARY OPTIC	2013-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.75	36.16	95.6	0.084	4.5	3.94	36656	36656			19

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	1.75	1.8	89.6		0.366	3.1	3.71

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1xg2	1.75	36.16	34821	1835	95.58	0.1725	0.171	0.2015	RANDOM	20.727

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]
0.9			-0.23		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.974
r_dihedral_angle_4_deg	16.627
r_dihedral_angle_3_deg	10.805
r_dihedral_angle_1_deg	6.366
r_mcangle_it	1.317
r_angle_refined_deg	1.305
r_mcbond_it	0.832
r_mcbond_other	0.831
r_angle_other_deg	0.746
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.974
r_dihedral_angle_4_deg	16.627
r_dihedral_angle_3_deg	10.805
r_dihedral_angle_1_deg	6.366
r_mcangle_it	1.317
r_angle_refined_deg	1.305
r_mcbond_it	0.832
r_mcbond_other	0.831
r_angle_other_deg	0.746
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2235
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	88

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
MrBUMP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.