6TJJ

Structure of Cerezyme at pH 4.6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62931.1 M (NH4)2SO4, 0.19 M guanidine HCl, 0.04 M KCl, 0.1 M Na acetate, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.2562.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.07α = 90
b = 285.865β = 90
c = 91.936γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.59142.931000.1470.0550.9987.27.91531796193710
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)RedundancyNumber Unique Reflections (All)
11.591.626.2022.3480.6760.57.974996

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2NT01.5977.442193668969899.9560.2160.21460.244832.082
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.178
r_dihedral_angle_other_1_deg35.453
r_dihedral_angle_4_deg16.146
r_dihedral_angle_3_deg14.737
r_dihedral_angle_1_deg7.578
r_lrange_it7.361
r_lrange_other7.345
r_scangle_it5.438
r_scangle_other5.438
r_scbond_it3.547
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.178
r_dihedral_angle_other_1_deg35.453
r_dihedral_angle_4_deg16.146
r_dihedral_angle_3_deg14.737
r_dihedral_angle_1_deg7.578
r_lrange_it7.361
r_lrange_other7.345
r_scangle_it5.438
r_scangle_other5.438
r_scbond_it3.547
r_scbond_other3.546
r_mcangle_other3.439
r_mcangle_it3.435
r_mcbond_it2.514
r_mcbond_other2.464
r_angle_refined_deg1.587
r_angle_other_deg1.36
r_nbd_refined0.208
r_symmetry_nbd_refined0.192
r_symmetry_nbd_other0.188
r_xyhbond_nbd_refined0.176
r_nbd_other0.17
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_refined0.166
r_symmetry_nbtor_other0.086
r_chiral_restr0.082
r_symmetry_xyhbond_nbd_other0.047
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7833
Nucleic Acid Atoms
Solvent Atoms715
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing