6TJJ

Structure of Cerezyme at pH 4.6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	1.1 M (NH4)2SO4, 0.19 M guanidine HCl, 0.04 M KCl, 0.1 M Na acetate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.07	α = 90
b = 285.865	β = 90
c = 91.936	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	100	PIXEL	DECTRIS EIGER2 X 16M		2018-10-11	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)	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	1.59	142.93	100	0.147	0.055	0.998	7.2	7.9	1531796	193710

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.59	1.62			6.202	2.348	0.676	0.5	7.9	74996

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2NT0	1.59	77.442	193668	9698	99.956	0.216	0.2146	0.2448	32.082

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]
4.921			-1.64		-3.281

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.178
r_dihedral_angle_other_1_deg	35.453
r_dihedral_angle_4_deg	16.146
r_dihedral_angle_3_deg	14.737
r_dihedral_angle_1_deg	7.578
r_lrange_it	7.361
r_lrange_other	7.345
r_scangle_it	5.438
r_scangle_other	5.438
r_scbond_it	3.547
r_scbond_other	3.546
r_mcangle_other	3.439
r_mcangle_it	3.435
r_mcbond_it	2.514
r_mcbond_other	2.464
r_angle_refined_deg	1.587
r_angle_other_deg	1.36
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.176
r_nbd_other	0.17
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.166
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7833
Nucleic Acid Atoms
Solvent Atoms	715
Heterogen Atoms	240

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing