3C0O

Crystal structure of the proaerolysin mutant Y221G complexed with mannose-6-phosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	291	9-11% PEG 4000, 100mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.954	α = 90
b = 90.78	β = 90
c = 165.805	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	PSI PILATUS 6M		2007-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.979	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	61.2	99.3	0.094	0.076	14.01	4.8	37597	37597

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	98.7		0.389	0.31	4.1	4.5	5385

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	3C0N	2.5	61.2	37534	1870	99.14	0.20658	0.20314	0.27377	RANDOM	23.63

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]
-0.13			0.28		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.379
r_dihedral_angle_4_deg	21.909
r_dihedral_angle_3_deg	18.178
r_dihedral_angle_1_deg	7.241
r_mcangle_it	2.488
r_scangle_it	2.48
r_angle_refined_deg	2.005
r_scbond_it	1.664
r_mcbond_it	1.581
r_nbtor_refined	0.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.379
r_dihedral_angle_4_deg	21.909
r_dihedral_angle_3_deg	18.178
r_dihedral_angle_1_deg	7.241
r_mcangle_it	2.488
r_scangle_it	2.48
r_angle_refined_deg	2.005
r_scbond_it	1.664
r_mcbond_it	1.581
r_nbtor_refined	0.342
r_nbd_refined	0.259
r_symmetry_vdw_refined	0.24
r_xyhbond_nbd_refined	0.221
r_symmetry_hbond_refined	0.133
r_chiral_restr	0.121
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7038
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	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.