X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QWY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.62951.2 M NaCl, 100 mM Sodium Acetate, 50 mg/mL Lyzozyme, 30% Glycerol for cryoprotection
Crystal Properties
Matthews coefficientSolvent content
1.9938.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.381α = 90
b = 77.381β = 90
c = 37.162γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray125CCDOXFORD TITAN CCD2021-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54056

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.613.499.40.2750.3130.1410.9134.14.315346
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6398.64.3365.4793.2710.2482.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.613.411455175199.160.238130.235910.28195RANDOM15.605
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]
-0.19-0.190.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.098
r_dihedral_angle_4_deg15.467
r_dihedral_angle_3_deg13.722
r_dihedral_angle_1_deg6.758
r_long_range_B_refined5.138
r_long_range_B_other4.941
r_scangle_other3.036
r_mcangle_other2.195
r_mcangle_it2.193
r_scbond_it1.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.098
r_dihedral_angle_4_deg15.467
r_dihedral_angle_3_deg13.722
r_dihedral_angle_1_deg6.758
r_long_range_B_refined5.138
r_long_range_B_other4.941
r_scangle_other3.036
r_mcangle_other2.195
r_mcangle_it2.193
r_scbond_it1.904
r_scbond_other1.902
r_mcbond_it1.585
r_angle_refined_deg1.547
r_angle_other_deg1.429
r_mcbond_other1.243
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing